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cvx-refs.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
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@article{le_bellec_12_2011,
author = {Le Bellec, Fabrice and Vaillant, Fabrice and Imbert, Eric},
date-added = {2025-01-15 10:13:10 -0600},
date-modified = {2025-01-15 10:13:20 -0600},
journal = {Fruits},
number = {4},
pages = {237--250},
publisher = {EDP Sciences},
title = {Pitahaya (Hylocereus spp.): a new fruit crop, a market with a future},
volume = {61},
year = {2006}}
@article{adams2004virology,
author = {Adams, MJ and Antoniw, JF and Bar-Joseph, M and Brunt, AA and Candresse, Thierry and Foster, GD and Martelli, GP and Milne, RG and Fauquet, CM},
date-added = {2025-01-15 09:57:30 -0600},
date-modified = {2025-01-15 10:00:16 -0600},
journal = {Archives of virology},
pages = {1045--1060},
publisher = {Springer},
title = {{Virology Division News: The} new plant virus family {Flexiviridae} and assessment of molecular criteria for species demarcation},
volume = {149},
year = {2004}}
@article{hammond2021sequence,
author = {Hammond, John and Adams, Ian P and Fowkes, Aimee R and McGreig, Sam and Botermans, Marleen and van Oorspronk, Joanieke JA and Westenberg, Marcel and Verbeek, Martin and Dullemans, Annette M and Stijger, Christina CMM and others},
date-added = {2023-12-06 18:34:08 -0600},
date-modified = {2023-12-06 18:34:08 -0600},
journal = {Plant Pathology},
number = {2},
pages = {249--258},
publisher = {Wiley Online Library},
title = {Sequence analysis of 43-year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributed},
volume = {70},
year = {2021}}
@article{Kim_2015,
author = {Kim, J. and Kil, E.‐J. and Kim, S. and Seo, H. and Byun, H.‐S. and Park, J. and Chung, M.‐N. and Kwak, H.‐R. and Kim, M.‐K. and Kim, C.‐S. and Yang, J.‐W. and Lee, K.‐Y. and Choi, H.‐S. and Lee, S.},
date-added = {2023-12-06 12:24:37 -0600},
date-modified = {2025-01-15 10:00:41 -0600},
doi = {10.1111/ppa.12366},
issn = {1365-3059},
journal = {Plant Pathology},
month = mar,
number = {6},
pages = {1284--1291},
publisher = {Wiley},
title = {Seed transmission of Sweet potato leaf curl virus in sweet potato {(Ipomoea batatas)}},
url = {http://dx.doi.org/10.1111/ppa.12366},
volume = {64},
year = {2015},
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@article{Hipper_2013,
author = {Hipper, Cl{\'e}mence and Brault, V{\'e}ronique and Ziegler-Graff, V{\'e}ronique and Revers, Fr{\'e}d{\'e}ric},
date-added = {2023-12-06 12:12:12 -0600},
date-modified = {2025-01-15 09:51:57 -0600},
doi = {10.3389/fpls.2013.00154},
issn = {1664-462X},
journal = {Frontiers in Plant Science},
publisher = {Frontiers Media SA},
title = {Viral and Cellular Factors Involved in Phloem Transport of Plant Viruses},
url = {http://dx.doi.org/10.3389/fpls.2013.00154},
volume = {4},
year = {2013},
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@article{murrell2013,
author = {Murrell, Ben and Moola, Sasha and Mabona, Amandla and Weighill, Thomas and Sheward, Daniel and Kosakovsky Pond, Sergei L and Scheffler, Konrad},
date-added = {2022-11-16 12:53:10 -0600},
date-modified = {2022-11-16 12:53:31 -0600},
journal = {Molecular Biology and Evolution},
number = {5},
pages = {1196--1205},
publisher = {Society for Molecular Biology and Evolution},
title = {FUBAR: a fast, unconstrained bayesian approximation for inferring selection},
volume = {30},
year = {2013}}
@article{bae2022first,
author = {Bae, Miah and Lee, Hyo-Jeong and Jeong, Rae-Dong and Park, Mi-Ri},
date-added = {2022-10-31 19:28:21 -0500},
date-modified = {2022-10-31 19:28:21 -0500},
journal = {Journal of Plant Pathology},
number = {3},
pages = {1137--1137},
publisher = {Springer},
title = {First report of cactus virus X infecting banana (Musa spp.) in Korea},
volume = {104},
year = {2022}}
@article{serdari2019automated,
author = {Serdari, Dora and Kostaki, Evangelia-Georgia and Paraskevis, Dimitrios and Stamatakis, Alexandros and Kapli, Paschalia},
date-added = {2022-10-31 19:19:06 -0500},
date-modified = {2022-10-31 19:19:06 -0500},
journal = {PeerJ},
pages = {e7754},
publisher = {PeerJ Inc.},
title = {Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV},
volume = {7},
year = {2019}}
@article{simmonds2018virus,
author = {Simmonds, Peter and Aiewsakun, Pakorn},
date-added = {2022-10-31 19:07:40 -0500},
date-modified = {2022-10-31 19:07:40 -0500},
journal = {Archives of virology},
number = {8},
pages = {2037--2046},
publisher = {Springer},
title = {Virus classification--where do you draw the line?},
volume = {163},
year = {2018}}
@article{Kapli_2017,
author = {P. Kapli and S. Lutteropp and J. Zhang and K. Kobert and P. Pavlidis and A. Stamatakis and T. Flouri},
date-added = {2022-10-27 14:44:44 -0500},
date-modified = {2025-01-15 09:59:28 -0600},
doi = {10.1093/bioinformatics/btx025},
journal = {Bioinformatics},
month = {jan},
pages = {btx025},
publisher = {Oxford University Press ({OUP})},
title = {Multi-rate Poisson Tree Processes for single-locus species delimitation under {Maximum Likelihood and Markov Chain Monte Carlo}.},
url = {https://doi.org/10.1093%2Fbioinformatics%2Fbtx025},
year = 2017,
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@article{Zhang_2013,
author = {Jiajie Zhang and Paschalia Kapli and Pavlos Pavlidis and Alexandros Stamatakis},
date-added = {2022-10-27 14:42:12 -0500},
date-modified = {2022-10-27 14:42:12 -0500},
doi = {10.1093/bioinformatics/btt499},
journal = {Bioinformatics},
month = {aug},
number = {22},
pages = {2869--2876},
publisher = {Oxford University Press ({OUP})},
title = {A general species delimitation method with applications to phylogenetic placements},
url = {https://doi.org/10.1093%2Fbioinformatics%2Fbtt499},
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abstract = {Two scientists contributed to the discovery of the first virus, Tobacco mosaic virus. Ivanoski reported in 1892 that extracts from infected leaves were still infectious after filtration through a Chamberland filter-candle. Bacteria are retained by such filters, a new world was discovered : filterable pathogens. However, Ivanovski probably did not grasp the full meaning of his discovery. Beijerinck, in 1898, was the first to call `virus', the incitant of the tobacco mosaic. He showed that the incitant was able to migrate in an agar gel, therefore being an infectious soluble agent, or a `contagium vivum fluidum' and definitively not a `contagium fixum' as would be a bacteria. Ivanovski and Beijerinck brought unequal but decisive and complementary contributions to the discovery of viruses. Since then, discoveries made on Tobacco mosaic virus have stood out as milestones of virology history.
R{\'e}sum{\'e}
Deux hommes ont contribu{\'e} {\`a} la d{\'e}couverte du premier virus, le virus de la mosa{\"\i}que du tabac. Ivanovski d{\'e}montre en 1892 qu'un extrait de feuille malade reste infectieux apr{\`e}s filtration {\`a} travers un filtre de Chamberland. Les bact{\'e}ries sont retenues par ces filtres, un nouveau monde est d{\'e}couvert : les agents pathog{\`e}nes filtrants. Mais Ivanovski n'a sans doute pas pris toute la mesure de sa d{\'e}couverte. Beijerinck, en 1898, sera le premier {\`a} appeler « virus », l'agent causal de la mosa{\"\i}que du tabac. Il d{\'e}montre sa diffusion dans un gel d'Agar, c'est un agent infectieux soluble ou contagium vivum fluidum, et non un contagium fixum comme le serait une bact{\'e}rie. Ivanovski et Beijerinck ont donc apport{\'e} des contributions, certes in{\'e}gales, mais essentielles et compl{\'e}mentaires {\`a} la d{\'e}couverte du premier virus. Depuis, les travaux sur le virus de la mosa{\"\i}que du tabac ont jalonn{\'e} l'histoire de la virologie.},
author = {Herv{\'e} Lecoq},
date-added = {2021-09-20 14:33:16 -0500},
date-modified = {2021-09-20 14:33:16 -0500},
doi = {https://doi.org/10.1016/S0764-4469(01)01368-3},
issn = {0764-4469},
journal = {Comptes Rendus de l'Acad{\'e}mie des Sciences - Series III - Sciences de la Vie},
keywords = {virology, , TMV, filterable pathogens, agent filtrant, virologie, virus de la mosa{\"\i}que du tabac},
number = {10},
pages = {929-933},
title = {D{\'e}couverte du premier virus, le virus de la mosa{\"\i}que du tabac : 1892 ou 1898 ?},
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volume = {324},
year = {2001},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0764446901013683},
bdsk-url-2 = {https://doi.org/10.1016/S0764-4469(01)01368-3}}
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date-modified = {2025-01-15 10:23:17 -0600},
journal = {Berichte der Deutschen botanischen Gesellschaft in Berlin},
pages = {195--202},
title = {{{\"U}ber merkw{\"u}rdige geformte Proteink{\"o}rper in den Zweigen von {\em Epiphyllum}}},
volume = {3},
year = {1885}}
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date-modified = {2021-09-20 13:50:24 -0500},
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title = {{\"U}ber die Mosaikkrankheit des Tabaks},
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year = {1886}}
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urldate = {2021-08-11},
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language = {en},
month = jun,
number = {6},
pages = {587--589},
shorttitle = {{ModelFinder}},
title = {{ModelFinder}: fast model selection for accurate phylogenetic estimates},
url = {http://www.nature.com/articles/nmeth.4285},
urldate = {2021-08-10},
volume = {14},
year = {2017},
bdsk-url-1 = {http://www.nature.com/articles/nmeth.4285},
bdsk-url-2 = {https://doi.org/10.1038/nmeth.4285}}
@article{chessin_distribution_1972,
author = {Chessin, M.},
doi = {10.1094/Phyto-62-97},
file = {Chessin - 1972 - Distribution of Cactus Viruses in Wild Plants.pdf:/Users/alexa/Zotero/storage/597UN6SM/Chessin - 1972 - Distribution of Cactus Viruses in Wild Plants.pdf:application/pdf},
issn = {0031949X},
journal = {Phytopathology},
language = {en},
number = {1},
pages = {97},
title = {Distribution of {Cactus} {Viruses} in {Wild} {Plants}},
url = {http://www.apsnet.org/publications/phytopathology/backissues/Documents/1972Abstracts/Phyto62_97.htm},
urldate = {2021-08-10},
volume = {62},
year = {1972},
bdsk-url-1 = {http://www.apsnet.org/publications/phytopathology/backissues/Documents/1972Abstracts/Phyto62_97.htm},
bdsk-url-2 = {https://doi.org/10.1094/Phyto-62-97}}
@article{peng_molecular_2016,
author = {Peng, C. and Yu, N. T. and Luo, Z. W. and Fan, H. Y. and He, F. and Li, X. H. and Zhang, Z. L. and Liu, Z. X.},
doi = {10.1094/PDIS-01-16-0048-PDN},
file = {Peng et al. - 2016 - Molecular Identification of Cactus virus X .pdf:/Users/alexa/Zotero/storage/RN92VLGT/Peng et al. - 2016 - Molecular Identification of Cactus virus X .pdf:application/pdf},
issn = {0191-2917, 1943-7692},
journal = {Plant Disease},
language = {en},
month = sep,
number = {9},
pages = {1956},
title = {Molecular {Identification} of {Cactus} virus {X} {Infecting} {Hylocereus} polyrhizus ({Cactaceae}) in {Hainan} {Island}, {China}},
url = {https://apsjournals.apsnet.org/doi/10.1094/PDIS-01-16-0048-PDN},
urldate = {2021-05-03},
volume = {100},
year = {2016},
bdsk-url-1 = {https://apsjournals.apsnet.org/doi/10.1094/PDIS-01-16-0048-PDN},
bdsk-url-2 = {https://doi.org/10.1094/PDIS-01-16-0048-PDN}}
@article{milbrath_isolation_1972,
author = {Milbrath, Gene M. and Nelson, Merritt R.},
file = {Phyto62n07_739.PDF:/Users/alexa/Zotero/storage/SFLLYIYV/Phyto62n07_739.PDF:application/pdf},
journal = {Phytopathology},
month = jul,
pages = {739--742},
title = {Isolation and {Characterization} of a {Virus} from {Saguaro} {Cactus}},
volume = {62},
year = {1972}}
@article{liou_complete_2004,
abstract = {The complete nucleotide sequence of a strain of Cactus virus X (CVXHu) isolated from Hylocereus undatus (Cactaceae) has been determined. Excluding the poly(A) tail, the sequence is 6614 nucleotides in length and contains seven open reading frames (ORFs). The genome organization of CVX is similar to that of other potexviruses. ORF1 encodes the putative viral replicase with conserved methyltransferase, helicase, and polymerase motifs. Within ORF1, two other ORFs were located separately in the +2 reading frame, we call these ORF6 and ORF7. ORF2, 3, and 4, which form the ``triple gene block'' characteristic of the potexviruses, encode proteins with molecular mass of 25, 12, and 7 KDa, respectively. ORF5 encodes the coat protein with an estimated molecular mass of 24 KDa. Sequence analysis indicated that proteins encoded by ORF1-5 display certain degree of homology to the corresponding proteins of other potexviruses. Putative product of ORF6, however, shows no significant similarity to those of other potexviruses. Phylogenetic analyses based on the replicase (the methyltransferase, helicase, and polymerase domains) and coat protein demonstrated a closer relationship of CVX with Bamboo mosaic virus, Cassava common mosaic virus, Foxtail mosaic virus, Papaya mosaic virus, and Plantago asiatica mosaic virus.},
author = {Liou, M. R. and Chen, Y. R. and Liou, R. F.},
date-modified = {2025-01-15 10:18:16 -0600},
doi = {10.1007/s00705-003-0251-1},
file = {Liou et al. - 2004 - Complete nucleotide sequence and genome organizati.pdf:/Users/alexa/Zotero/storage/KHLU3U3H/Liou et al. - 2004 - Complete nucleotide sequence and genome organizati.pdf:application/pdf},
issn = {0304-8608, 1432-8798},
journal = {Archives of Virology},
language = {en},
month = may,
number = {5},
pages = {1037--1043},
title = {Complete nucleotide sequence and genome organization of a {Cactus} virus {X} strain from \textit{{Hylocereus} undatus} ({Cactaceae})},
url = {http://link.springer.com/10.1007/s00705-003-0251-1},
urldate = {2021-05-03},
volume = {149},
year = {2004},
bdsk-url-1 = {http://link.springer.com/10.1007/s00705-003-0251-1},
bdsk-url-2 = {https://doi.org/10.1007/s00705-003-0251-1}}
@article{casper_new_1969,
author = {Casper, R and Brandes, J},
file = {casper1969.pdf:/Users/alexa/Zotero/storage/3G42ANLR/casper1969.pdf:application/pdf},
journal = {J. gen. Virol.},
pages = {155--156},
title = {A {New} {Cactus} {Virus}},
volume = {5},
year = {1969}}
@article{park_detection_2018,
author = {Park, Chung Hwa and Song, Eun Gyeong and Ryu, Ki Hyun},
doi = {10.5423/PPJ.NT.08.2017.0187},
file = {Park et al. - 2018 - Detection of Co-Infection of Notocactus leninghaus.pdf:/Users/alexa/Zotero/storage/AZJ65EH5/Park et al. - 2018 - Detection of Co-Infection of Notocactus leninghaus.pdf:application/pdf},
issn = {1598-2254, 2093-9280},
journal = {The Plant Pathology Journal},
language = {en},
month = feb,
number = {1},
pages = {65--70},
title = {Detection of {Co}-{Infection} of {Notocactus} leninghausii f. cristatus with {Six} {Virus} {Species} in {South} {Korea}},
url = {http://ppjonline.org/journal/view.php?doi=10.5423/PPJ.NT.08.2017.0187},
urldate = {2021-05-02},
volume = {34},
year = {2018},
bdsk-url-1 = {http://ppjonline.org/journal/view.php?doi=10.5423/PPJ.NT.08.2017.0187},
bdsk-url-2 = {https://doi.org/10.5423/PPJ.NT.08.2017.0187}}
@article{maarsingh_comparative_2019,
abstract = {Background: Mycobacterium smegmatis is a saprophytic bacterium frequently used as a genetic surrogate to study pathogenic Mycobacterium tuberculosis. The PrrAB two-component genetic regulatory system is essential in M. tuberculosis and represents an attractive therapeutic target. In this study, transcriptomic analysis (RNA-seq) of an M. smegmatis ΔprrAB mutant was used to define the PrrAB regulon and provide insights into the essential nature of PrrAB in M. tuberculosis.
Results: RNA-seq differential expression analysis of M. smegmatis wild-type (WT), ΔprrAB mutant, and complementation strains revealed that during in vitro exponential growth, PrrAB regulates 167 genes (q {\textless} 0.05), 57\% of which are induced in the WT background. Gene ontology and cluster of orthologous groups analyses showed that PrrAB regulates genes participating in ion homeostasis, redox balance, metabolism, and energy production. PrrAB induced transcription of dosR (devR), a response regulator gene that promotes latent infection in M. tuberculosis and 21 of the 25 M. smegmatis DosRS regulon homologues. Compared to the WT and complementation strains, the ΔprrAB mutant exhibited an exaggerated delayed growth phenotype upon exposure to potassium cyanide and respiratory inhibition. Gene expression profiling correlated with these growth deficiency results, revealing that PrrAB induces transcription of the high-affinity cytochrome bd oxidase genes under both aerobic and hypoxic conditions. ATP synthesis was {\textasciitilde} 64\% lower in the ΔprrAB mutant relative to the WT strain, further demonstrating that PrrAB regulates energy production.
Conclusions: The M. smegmatis PrrAB two-component system regulates respiratory and oxidative phosphorylation pathways, potentially to provide tolerance against the dynamic environmental conditions experienced in its natural ecological niche. PrrAB positively regulates ATP levels during exponential growth, presumably through transcriptional activation of both terminal respiratory branches (cytochrome c bc1-aa3 and cytochrome bd oxidases), despite transcriptional repression of ATP synthase genes. Additionally, PrrAB positively regulates expression of the dormancy-associated dosR response regulator genes in an oxygen-independent manner, which may serve to finetune sensory perception of environmental stimuli associated with metabolic repression.},
author = {Maarsingh, Jason D. and Yang, Shanshan and Park, Jin G. and Haydel, Shelley E.},
doi = {10.1186/s12864-019-6105-3},
file = {Maarsingh et al. - 2019 - Comparative transcriptomics reveals PrrAB-mediated.pdf:/Users/alexa/Zotero/storage/Q45JXXUT/Maarsingh et al. - 2019 - Comparative transcriptomics reveals PrrAB-mediated.pdf:application/pdf},
issn = {1471-2164},
journal = {BMC Genomics},
language = {en},
month = dec,
number = {1},
pages = {942},
title = {Comparative transcriptomics reveals {PrrAB}-mediated control of metabolic, respiration, energy-generating, and dormancy pathways in {Mycobacterium} smegmatis},
url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6105-3},
urldate = {2021-05-02},
volume = {20},
year = {2019},
bdsk-url-1 = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6105-3},
bdsk-url-2 = {https://doi.org/10.1186/s12864-019-6105-3}}
@article{koenig_molecular_2004,
author = {Koenig, R. and Aust, H. and Schiemann, J. and Pleij, C. W. A. and Loss, S. and Burgermeister, W.},
doi = {10.1007/s00705-003-0268-5},
file = {Koenig et al. - 2004 - Molecular characterisation of potexviruses isolate.pdf:/Users/alexa/Zotero/storage/5JU4LIHI/Koenig et al. - 2004 - Molecular characterisation of potexviruses isolate.pdf:application/pdf},
issn = {0304-8608, 1432-8798},
journal = {Archives of Virology},
language = {en},
month = may,
number = {5},
pages = {903--914},
title = {Molecular characterisation of potexviruses isolated from three different genera in the family {Cactaceae}},
url = {http://link.springer.com/10.1007/s00705-003-0268-5},
urldate = {2021-05-01},
volume = {149},
year = {2004},
bdsk-url-1 = {http://link.springer.com/10.1007/s00705-003-0268-5},
bdsk-url-2 = {https://doi.org/10.1007/s00705-003-0268-5}}
@article{evallo_brief_2021,
abstract = {Plant pathogens, including viruses, have a known negative impact on plant growth and development. Here, plant diseases caused by cactus virus X (CVX) are reviewed. CVX infects a range of plant species within the Cactaceae family. When expressed, symptoms include chlorosis, necrosis, and morphological alterations, such as the twisting of arms, but at times plants can be asymptomatic. CVX may be transmitted through contaminated grafting or cutting tools and can also occur as mixed infections with other viruses, including zygocactus virus X and pitaya virus X. CVX may also play a role in altering the plant's physiology. The virus can be detected by molecular assays, including polymerase chain reaction (PCR), and transmitted to indicator plants. Sanitation in both nurseries and fields is critical in controlling the spread of CVX. This paper highlights CVX as a potential production threat to some Cactaceae family members, particularly the now popular Hylocereus species or dragon fruits.},
author = {Evallo, Edzel and Taguiam, John Darby and Balendres, Mark Angelo},
doi = {10.1016/j.cropro.2021.105566},
file = {Evallo et al. - 2021 - A brief review of plant diseases caused by Cactus .pdf:/Users/alexa/Zotero/storage/5K3KE92R/Evallo et al. - 2021 - A brief review of plant diseases caused by Cactus .pdf:application/pdf},
issn = {02612194},
journal = {Crop Protection},
language = {en},
month = may,
pages = {105566},
title = {A brief review of plant diseases caused by {Cactus} virus {X}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0261219421000363},
urldate = {2021-04-30},
volume = {143},
year = {2021},
bdsk-url-1 = {https://linkinghub.elsevier.com/retrieve/pii/S0261219421000363},
bdsk-url-2 = {https://doi.org/10.1016/j.cropro.2021.105566}}
@article{hunt_contributions_1969,
author = {Hunt, D. R.},
doi = {10.2307/4108963},
issn = {00755974},
journal = {Kew Bulletin},
number = {2},
pages = {255},
shorttitle = {Contributions to the {Flora} of {Tropical} {America}},
title = {Contributions to the {Flora} of {Tropical} {America}: {LXXVII}: {A} {Synopsis} of {Schlumbergera} {Lem}. ({Cactaceae})},
url = {https://www.jstor.org/stable/4108963?origin=crossref},
urldate = {2021-04-28},
volume = {23},
year = {1969},
bdsk-url-1 = {https://www.jstor.org/stable/4108963?origin=crossref},
bdsk-url-2 = {https://doi.org/10.2307/4108963}}
@article{delwart_viral_2007,
abstract = {Characterisation of new viruses is often hindered by difficulties in amplifying them in cell culture, limited antigenic/ serological cross-reactivity or the lack of nucleic acid hybridisation to known viral sequences. Numerous molecular methods have been used to genetically characterise new viruses without prior in vitro replication or the use of virusspecific reagents. In the recent metagenomic studies viral particles from uncultured environmental and clinical samples have been purified and their nucleic acids randomly amplified prior to subcloning and sequencing. Already known and novel viruses were then identified by comparing their translated sequence to those of viral proteins in public sequence databases. Metagenomic approaches to viral characterisation have been applied to seawater, near shore sediments, faeces, serum, plasma and respiratory secretions and have broadened the range of known viral diversity. Selection of samples with high viral loads, purification of viral particles, removal of cellular nucleic acids, efficient sequence-independent amplification of viral RNA and DNA, recognisable sequence similarities to known viral sequences and deep sampling of the nucleic acid populations through large scale sequencing can all improve the yield of new viruses. This review lists some of the animal viruses recently identified using sequence-independent methods, current laboratory and bioinformatics methods, together with their limitations and potential improvements. Viral metagenomic approaches provide novel opportunities to generate an unbiased characterisation of the viral populations in various organisms and environments. Copyright \# 2007 John Wiley \& Sons, Ltd.},
author = {Delwart, Eric L.},
doi = {10.1002/rmv.532},
file = {Delwart - 2007 - Viral metagenomics.pdf:/Users/alexa/Zotero/storage/ENIKDTSC/Delwart - 2007 - Viral metagenomics.pdf:application/pdf},
issn = {10529276, 10991654},
journal = {Reviews in Medical Virology},
language = {en},
month = mar,
number = {2},
pages = {115--131},
title = {Viral metagenomics},
url = {https://onlinelibrary.wiley.com/doi/10.1002/rmv.532},
urldate = {2021-08-30},
volume = {17},
year = {2007},
bdsk-url-1 = {https://onlinelibrary.wiley.com/doi/10.1002/rmv.532},
bdsk-url-2 = {https://doi.org/10.1002/rmv.532}}
@article{valente_correlates_2014,
author = {Valente, Luis M. and Britton, Adam W. and Powell, Martyn P. and Papadopulos, Alexander S. T. and Burgoyne, Priscilla M. and Savolainen, Vincent},
doi = {10.1111/boj.12117},
file = {Valente et al. - 2014 - Correlates of hyperdiversity in southern African i.pdf:/Users/alexa/Zotero/storage/2SYGTWSQ/Valente et al. - 2014 - Correlates of hyperdiversity in southern African i.pdf:application/pdf},
issn = {00244074},
journal = {Botanical Journal of the Linnean Society},
language = {en},
month = jan,
number = {1},
pages = {110--129},
shorttitle = {Correlates of hyperdiversity in southern {African} ice plants ({Aizoaceae})},
title = {Correlates of hyperdiversity in southern {African} ice plants ({Aizoaceae}): {Diversification} in {Aizoaceae}},
url = {https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/boj.12117},
urldate = {2021-08-30},
volume = {174},
year = {2014},
bdsk-url-1 = {https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/boj.12117},
bdsk-url-2 = {https://doi.org/10.1111/boj.12117}}
@article{lefeuvre2019,
abstract = {The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80\% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review , we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics.},
author = {Lefeuvre, Pierre and Martin, Darren P. and Elena, Santiago F. and Shepherd, Dionne N. and Roumagnac, Philippe and Varsani, Arvind},
date-modified = {2022-03-05 17:12:50 -0800},
doi = {10.1038/s41579-019-0232-3},
issn = {1740-1526, 1740-1534},
journal = {Nature Reviews Microbiology},
language = {en},
month = oct,
number = {10},
pages = {632--644},
title = {Evolution and ecology of plant viruses},
url = {http://www.nature.com/articles/s41579-019-0232-3},
urldate = {2021-08-30},
volume = {17},
year = {2019},
bdsk-url-1 = {http://www.nature.com/articles/s41579-019-0232-3},
bdsk-url-2 = {https://doi.org/10.1038/s41579-019-0232-3}}
@article{one_thousand_plant_transcriptomes_initiative_one_2019,
abstract = {Abstract
Green plants (Viridiplantae) include around 450,000--500,000 species
1,2
of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.},
author = {{One Thousand Plant Transcriptomes Initiative}},
doi = {10.1038/s41586-019-1693-2},
file = {One Thousand Plant Transcriptomes Initiative - 2019 - One thousand plant transcriptomes and the phylogen.pdf:/Users/alexa/Zotero/storage/MW7FEVNI/One Thousand Plant Transcriptomes Initiative - 2019 - One thousand plant transcriptomes and the phylogen.pdf:application/pdf},
issn = {0028-0836, 1476-4687},
journal = {Nature},
language = {en},
month = oct,
number = {7780},
pages = {679--685},
title = {One thousand plant transcriptomes and the phylogenomics of green plants},
url = {http://www.nature.com/articles/s41586-019-1693-2},
urldate = {2021-08-30},
volume = {574},
year = {2019},
bdsk-url-1 = {http://www.nature.com/articles/s41586-019-1693-2},
bdsk-url-2 = {https://doi.org/10.1038/s41586-019-1693-2}}
@article{koonin1993,
abstract = {Despite the rapid mutational change that is typical of positive-strand RNA viruses, enzymes mediating the replication and expression of virus genomes contain arrays of conserved sequence motifs. Proteins with such motifs include RNA-dependent RNA polymerase, putative RNA helicase, chymotrypsin-like and papain-like proteases, and methyltransferases. The genes for these proteins form partially conserved modules in large subsets of viruses. A concept of the virus genome as a relatively evolutionarily stable ``core'' of housekeeping genes accompaniedby a much more flexible``shell'' consisting mostly of genes coding for virion components and various accessory proteins is discussed. Shuffling of the ``shell'' genes including genome reorganization and recombination between remote groups of viruses is considered to be one of the major factors of virus evolution. Multiple alignments for the conserved viral proteins were constructed and used to generate the respective phylogenetic trees. Based primarily on the tentative phylogeny for the RNA-dependent RNA polymerase, which is the only universally conserved protein of positive-strand RNA viruses, three large classes of viruses, each consisting of distinct smaller divisions, were delineated. A strong correlation was observed between this grouping and the tentative phylogenies for the other conserved proteins as well as the arrangement of genes encoding these proteins in the virus genome. A comparable correlation with the polymerase phylogeny was not found for genes encoding virion components or for genome expression strategies. It is surmised that several types of arrangement of the ``shell'' genes as well as basic mechanisms of expression could have evolved independently in different evolutionary lineages. The grouping revealed by phylogeneticanalysismay provide the basis for revision of virus classification,and phylogenetictaxonomy of positive-strandRNA viruses is outlined. Someof the phylogenetically derived divisions of positive-strandRNA viruses also include double-strandedRNA viruses, indicating that in certain cases the type of genome nucleic acid may not be a reliable taxonomic criterion for viruses.},
author = {Koonin, Eugene V. and Dolja, Valerian V. and Morris, T. Jack},
date-modified = {2022-03-05 17:13:49 -0800},
doi = {10.3109/10409239309078440},
file = {Koonin et al. - 1993 - Evolution and Taxonomy of Positive-Strand RNA Viru.pdf:/Users/alexa/Zotero/storage/2AW9IDNW/Koonin et al. - 1993 - Evolution and Taxonomy of Positive-Strand RNA Viru.pdf:application/pdf},
issn = {1040-9238, 1549-7798},
journal = {Critical Reviews in Biochemistry and Molecular Biology},
language = {en},
month = jan,
number = {5},
pages = {375--430},
shorttitle = {Evolution and {Taxonomy} of {Positive}-{Strand} {RNA} {Viruses}},
title = {Evolution and {Taxonomy} of {Positive}-{Strand} {RNA} {Viruses}: {Implications} of {Comparative} {Analysis} of {Amino} {Acid} {Sequences}},
url = {http://www.tandfonline.com/doi/full/10.3109/10409239309078440},
urldate = {2021-08-30},
volume = {28},
year = {1993},
bdsk-url-1 = {http://www.tandfonline.com/doi/full/10.3109/10409239309078440},
bdsk-url-2 = {https://doi.org/10.3109/10409239309078440}}
@article{schulz_towards_2017,
abstract = {The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts.},
author = {Schulz, Frederik and Eloe-Fadrosh, Emiley A. and Bowers, Robert M. and Jarett, Jessica and Nielsen, Torben and Ivanova, Natalia N. and Kyrpides, Nikos C. and Woyke, Tanja},
doi = {10.1186/s40168-017-0360-9},
file = {Schulz et al. - 2017 - Towards a balanced view of the bacterial tree of l.pdf:/Users/alexa/Zotero/storage/DW2TMFUK/Schulz et al. - 2017 - Towards a balanced view of the bacterial tree of l.pdf:application/pdf},
issn = {2049-2618},
journal = {Microbiome},
language = {en},
month = dec,
number = {1},
pages = {140},
title = {Towards a balanced view of the bacterial tree of life},
url = {https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0360-9},
urldate = {2021-08-31},
volume = {5},
year = {2017},
bdsk-url-1 = {https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0360-9},
bdsk-url-2 = {https://doi.org/10.1186/s40168-017-0360-9}}
@article{hug_new_2016,
author = {Hug, Laura A. and Baker, Brett J. and Anantharaman, Karthik and Brown, Christopher T. and Probst, Alexander J. and Castelle, Cindy J. and Butterfield, Cristina N. and Hernsdorf, Alex W. and Amano, Yuki and Ise, Kotaro and Suzuki, Yohey and Dudek, Natasha and Relman, David A. and Finstad, Kari M. and Amundson, Ronald and Thomas, Brian C. and Banfield, Jillian F.},
doi = {10.1038/nmicrobiol.2016.48},
file = {Hug et al. - 2016 - A new view of the tree of life.pdf:/Users/alexa/Zotero/storage/9K2YN9BS/Hug et al. - 2016 - A new view of the tree of life.pdf:application/pdf},
issn = {2058-5276},
journal = {Nature Microbiology},
language = {en},
month = may,
number = {5},
pages = {16048},
title = {A new view of the tree of life},
url = {http://www.nature.com/articles/nmicrobiol201648},
urldate = {2021-08-31},
volume = {1},
year = {2016},
bdsk-url-1 = {http://www.nature.com/articles/nmicrobiol201648},
bdsk-url-2 = {https://doi.org/10.1038/nmicrobiol.2016.48}}
@article{gregory_marine_2019,
abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.},
author = {Gregory, Ann C. and Zayed, Ahmed A. and Concei{\c c}{\~a}o-Neto, N{\'a}dia and Temperton, Ben and Bolduc, Ben and Alberti, Adriana and Ardyna, Mathieu and Arkhipova, Ksenia and Carmichael, Margaux and Cruaud, Corinne and Dimier, C{\'e}line and Dom{\'\i}nguez-Huerta, Guillermo and Ferland, Joannie and Kandels, Stefanie and Liu, Yunxiao and Marec, Claudie and Pesant, St{\'e}phane and Picheral, Marc and Pisarev, Sergey and Poulain, Julie and Tremblay, Jean-{\'E}ric and Vik, Dean and Acinas, Silvia G. and Babin, Marcel and Bork, Peer and Boss, Emmanuel and Bowler, Chris and Cochrane, Guy and de Vargas, Colomban and Follows, Michael and Gorsky, Gabriel and Grimsley, Nigel and Guidi, Lionel and Hingamp, Pascal and Iudicone, Daniele and Jaillon, Olivier and Kandels-Lewis, Stefanie and Karp-Boss, Lee and Karsenti, Eric and Not, Fabrice and Ogata, Hiroyuki and Pesant, St{\'e}phane and Poulton, Nicole and Raes, Jeroen and Sardet, Christian and Speich, Sabrina and Stemmann, Lars and Sullivan, Matthew B. and Sunagawa, Shinichi and Wincker, Patrick and Babin, Marcel and Bowler, Chris and Culley, Alexander I. and de Vargas, Colomban and Dutilh, Bas E. and Iudicone, Daniele and Karp-Boss, Lee and Roux, Simon and Sunagawa, Shinichi and Wincker, Patrick and Sullivan, Matthew B.},
date-modified = {2025-01-15 09:46:08 -0600},
doi = {10.1016/j.cell.2019.03.040},
file = {ScienceDirect Full Text PDF:/Users/alexa/Zotero/storage/IE89EYZT/Gregory et al. - 2019 - Marine DNA Viral Macro- and Microdiversity from Po.pdf:application/pdf},
issn = {0092-8674},
journal = {Cell},
keywords = {community ecology, diversity gradients, marine biology, metagenomics, population ecology, species, viruses},
language = {en},
month = may,
number = {5},
pages = {1109--1123},
title = {Marine {DNA} {Viral} {Macro}- and {Microdiversity} from {Pole} to {Pole}},
url = {https://www.sciencedirect.com/science/article/pii/S0092867419303411},
urldate = {2021-09-01},
volume = {177},
year = {2019},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0092867419303411},
bdsk-url-2 = {https://doi.org/10.1016/j.cell.2019.03.040}}
@article{martelli_family_2007,
abstract = {The plant virus family Flexiviridae includes the definitive genera Potexvirus, Mandarivirus, Allexivirus, Carlavirus, Foveavirus, Capillovirus, Vitivirus, Trichovirus, the putative genus Citrivirus, and some unassigned species. Its establishment was based on similarities in virion morphology, common features in genome type and organization, and strong phylogenetic relationships between replicational and structural proteins. In this review, we provide a brief account of the main biological and molecular properties of the members of the family, with special emphasis on the relationships within and among the genera. In phylogenetic analyses the potexvirus-like replicases were more closely related to tymoviruses than to carlaviruses. We postulate a common evolutionary ancestor for the family Tymoviridae and the two distinct evolutionary clusters of the Flexiviridae, i.e., a plant virus with a polyadenylated genome, filamentous virions, and a triple gene block of movement proteins. Subsequent recombination and gene loss would then have generated a very diverse group of plant and fungal viruses.},
author = {Martelli, Giovanni P. and Adams, Michael J. and Kreuze, Jan F. and Dolja, Valerian V.},
doi = {10.1146/annurev.phyto.45.062806.094401},
file = {Martelli et al. - 2007 - Family Flexiviridae A Case Study in Virio.pdf:/Users/alexa/Zotero/storage/7LK5VDLT/Martelli et al. - 2007 - Family Flexiviridae A Case Study in Virio.pdf:application/pdf},
issn = {0066-4286, 1545-2107},
journal = {Annual Review of Phytopathology},
language = {en},
month = sep,
number = {1},
pages = {73--100},
shorttitle = {Family \textit{{Flexiviridae}}},
title = {Family \textit{{Flexiviridae}} : {A} {Case} {Study} in {Virion} and {Genome} {Plasticity}},
url = {http://www.annualreviews.org/doi/10.1146/annurev.phyto.45.062806.094401},
urldate = {2021-09-01},
volume = {45},
year = {2007},
bdsk-url-1 = {http://www.annualreviews.org/doi/10.1146/annurev.phyto.45.062806.094401},
bdsk-url-2 = {https://doi.org/10.1146/annurev.phyto.45.062806.094401}}
@article{kreuze_ictv_2020,
abstract = {The family
Alphaflexiviridae
includes viruses with flexuous filamentous virions that are 470--800 nm in length and 12--13 nm in diameter. Alphaflexiviruses have a single-stranded, positive-sense RNA genome of 5.5--9 kb. They infect plants and plant-infecting fungi. They share a distinct lineage of alphavirus-like replication proteins that is unusual in lacking any recognized protease domain. With a single exception, cell-to-cell and long-distance movement is facilitated by triple gene block proteins in plant-infecting genera. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family
Alphaflexiviridae,
which is available at
www.ictv.global/report/alphaflexiviridae
.},
author = {Kreuze, Jan F. and Vaira, Anna Maria and Menzel, Wulf and Candresse, Thierry and Zavriev, Sergey K. and Hammond, John and Hyun Ryu, Ki and Report Consortium, Ictv},
doi = {10.1099/jgv.0.001436},
file = {Full Text:/Users/alexa/Zotero/storage/T7536UV2/Kreuze et al. - 2020 - ICTV Virus Taxonomy Profile Alphaflexiviridae.pdf:application/pdf},
issn = {0022-1317, 1465-2099},
journal = {Journal of General Virology},
language = {en},
month = jul,
number = {7},
pages = {699--700},
shorttitle = {{ICTV} {Virus} {Taxonomy} {Profile}},
title = {{ICTV} {Virus} {Taxonomy} {Profile}: {Alphaflexiviridae}},
url = {https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001436},
urldate = {2021-09-01},
volume = {101},
year = {2020},
bdsk-url-1 = {https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001436},
bdsk-url-2 = {https://doi.org/10.1099/jgv.0.001436}}
@article{korotkova_phylogenetic_2017,
abstract = {The tribe Hylocereeae are represented by mainly Central American-Mexican epiphytic, hemi-epiphytic and climbing cacti. They are popular due to their spectacular nocturnal flowers and have some importance as crops grown for their edible fruits. We present the first comprehensive phylogenetic study of the Hylocereeae sampling 60 out of the 63 currently accepted species and 17 out of 19 infraspecific taxa. Based on four plastid regions (trnK/matK, the rpl16 intron, rps3-rpl16, and trnL-F) we find a highly supported core Hylocereeae clade that also includes Acanthocereus and Peniocereus p.p., while Strophocactus is depicted as polyphyletic and is resolved outside of the Hylocereeae tribe. The clades found within Hylocereeae agree, in general terms, with the currently accepted genera but none of the genera are entirely monophyletic in their current circumscription. A new concept for the Hylocereeae is presented to include the genera Acanthocereus (incl. Peniocereus p.p.), Aporocactus, Disocactus, Epiphyllum, Selenicereus (incl. Hylocereus and Weberocereus p.p.), Pseudorhipsalis, Kimnachia gen. nov., and Weberocereus. New nomenclatural combinations are provided to make these genera monophyletic. The genus Deamia is reinstated for Strophocactus testudo and S. chontalensis, while Strophocactus is newly circumscribed to include S. wittii, Pseudoacanthocereus brasiliensis, and P. sicariguensis. Both genera are excluded from Hylocereeae. A taxonomic synopsis of Hylocereeae is provided.},
author = {Korotkova, Nadja and Borsch, Thomas and Arias, Salvador},
date-modified = {2025-01-15 10:02:22 -0600},
doi = {10.11646/phytotaxa.327.1.1},
file = {Korotkova et al. - 2017 - A phylogenetic framework for the Hylocereeae (Cact.pdf:/Users/alexa/Zotero/storage/WVM8KUHR/Korotkova et al. - 2017 - A phylogenetic framework for the Hylocereeae (Cact.pdf:application/pdf},
issn = {1179-3163, 1179-3155},
journal = {Phytotaxa},
language = {en},
month = nov,
number = {1},
pages = {1-46},
title = {A phylogenetic framework for the {Hylocereeae} ({Cactaceae}) and implications for the circumscription of the genera},
url = {https://biotaxa.org/Phytotaxa/article/view/phytotaxa.327.1.1},
urldate = {2021-09-01},
volume = {327},
year = {2017},
bdsk-url-1 = {https://biotaxa.org/Phytotaxa/article/view/phytotaxa.327.1.1},
bdsk-url-2 = {https://doi.org/10.11646/phytotaxa.327.1.1}}
@article{guerrero_phylogenetic_2019,
abstract = {Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here, we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.},
author = {Guerrero, Pablo C and Majure, Lucas C and Cornejo-Romero, Amelia and Hern{\'a}ndez-Hern{\'a}ndez, Tania},
doi = {10.1093/jhered/esy064},
file = {Guerrero et al. - 2019 - Phylogenetic Relationships and Evolutionary Trends.pdf:/Users/alexa/Zotero/storage/E88RU5H5/Guerrero et al. - 2019 - Phylogenetic Relationships and Evolutionary Trends.pdf:application/pdf},
issn = {0022-1503, 1465-7333},
journal = {Journal of Heredity},
language = {en},
month = jan,
number = {1},
pages = {4--21},
title = {Phylogenetic {Relationships} and {Evolutionary} {Trends} in the {Cactus} {Family}},
url = {https://academic.oup.com/jhered/article/110/1/4/5205122},
urldate = {2021-09-01},
volume = {110},
year = {2019},
bdsk-url-1 = {https://academic.oup.com/jhered/article/110/1/4/5205122},
bdsk-url-2 = {https://doi.org/10.1093/jhered/esy064}}
@article{shi_redefining_2016,
author = {Shi, Mang and Lin, Xian-Dan and Tian, Jun-Hua and Chen, Liang-Jun and Chen, Xiao and Li, Ci-Xiu and Qin, Xin-Cheng and Li, Jun and Cao, Jian-Ping and Eden, John-Sebastian and Buchmann, Jan and Wang, Wen and Xu, Jianguo and Holmes, Edward C. and Zhang, Yong-Zhen},
doi = {10.1038/nature20167},
file = {Shi et al. - 2016 - Redefining the invertebrate RNA virosphere.pdf:/Users/alexa/Zotero/storage/ARVDYPD9/Shi et al. - 2016 - Redefining the invertebrate RNA virosphere.pdf:application/pdf},
issn = {0028-0836, 1476-4687},
journal = {Nature},
language = {en},
month = dec,
number = {7634},
pages = {539--543},
title = {Redefining the invertebrate {RNA} virosphere},
url = {http://www.nature.com/articles/nature20167},
urldate = {2021-09-01},
volume = {540},
year = {2016},
bdsk-url-1 = {http://www.nature.com/articles/nature20167},
bdsk-url-2 = {https://doi.org/10.1038/nature20167}}
@article{campbell_shortening_1961,
author = {Campbell, A. I.},
doi = {10.1038/191517a0},
file = {Campbell - 1961 - Shortening the Juvenile Phase of Apple Seedlings.pdf:/Users/alexa/Zotero/storage/8QDYXJHH/Campbell - 1961 - Shortening the Juvenile Phase of Apple Seedlings.pdf:application/pdf},
issn = {0028-0836, 1476-4687},
journal = {Nature},
language = {en},
month = jul,
number = {4787},
pages = {517--517},
title = {Shortening the {Juvenile} {Phase} of {Apple} {Seedlings}},
url = {http://www.nature.com/articles/191517a0},
urldate = {2021-09-03},
volume = {191},
year = {1961},
bdsk-url-1 = {http://www.nature.com/articles/191517a0},
bdsk-url-2 = {https://doi.org/10.1038/191517a0}}
@article{duarte_potexvirus_2008,
abstract = {Northwestern Brazil is a major center of diversity for cactaceous plants, most of which are grown as ornamentals. Cactus virus X (CVX), the only virus reported so far from Brazilian cactaceae, is widely spread. In this study we have characterized viruses of Opuntia tuna (OT), Hylocereus undatus (HU) and Schlumbergera truncata (ST) from the State of S{\~a}o Paulo, showing chlorotic spots and mosaic symptoms. Mechanically inoculated Gomphrena globosa reacted with local lesions, except when OT extracts were used as inoculum, whereas Chenopodium amaranticolor showed erratic systemic symptoms following inoculations from HU and ST. Transmission electron microscopy showed flexuous particles ca. 550 nm in length and bundles of virus particles in leaf cells from naturally and experimentally infected plants. Virus particles reacted faintly with an antiserum to CVX. Nucleotide sequences of the RNA dependent RNA polymerase gene obtained from cloned RT-PCR products, revealed the occurrence of Zygocactus virus X (ZyVX) in OT, mixed infection by ZyVX and Schlumbergera virus X (SchVX) in HU, and mixed infection by ZyVX, SchVX and Opuntia virus X (OpVX) in ST. This is the first report of ZyVX, SchVX and OpVX in Brazil.},
author = {Duarte, L M L and Alexandre, M A V and Rivas, E B and Harakava, R and Galleti, S R and Barradas, M M},
file = {Duarte et al. - 2008 - POTEXVIRUS DIVERSITY IN CACTACEAE FROM S{\~A}O PAULO S.pdf:/Users/alexa/Zotero/storage/D2VM74WI/Duarte et al. - 2008 - POTEXVIRUS DIVERSITY IN CACTACEAE FROM S{\~A}O PAULO S.pdf:application/pdf},
journal = {Journal of Plant Pathology},
language = {en},
pages = {9},
title = {{POTEXVIRUS} {DIVERSITY} {IN} {CACTACEAE} {FROM} {S{\~A}O} {PAULO} {STATE} {IN} {BRAZIL}},
year = {2008}}
@article{maliarenko_cactus_2013,
abstract = {In plants of Cactaceae A. L. Juss. family occurrence of fasciated shoots and cristation of stems is often observed. Many studies have shown differences in the intensity of expression growth factors and genes associated with fasciation (cristation). We tested nine samples on viral infection, including Mammillaria elongata A. P. de Candolle f. cristata, growing on their own roots. The Scions: Mammillaria elongata A. P. de Candolle f. cristata, Echinopsis chamaecereus H. Friedr. \& Glaetzle f. cristata, Echinocereus pectinatus (Scheidw.) Eng. f. cristata, Echinopsis sp. Zucc. f. cristata which grow on the stocks Eriocereus jusbertii (Rebut) A. Berg., Echinopsis macrogona (Salm-Dyck). Basing on bioassay and morphological properties the detected viruses are related to Cactus virus 2 and Cactus virus X and genus Tobamovirus. As the same viral particles were found in the scions and stocks, we can assume that viruses cannot cause fasciation in the investigated species.},
author = {Maliarenko, Valentyna M. and Mudrak, Tatyana P.},
doi = {10.6001/biologija.v59i2.2754},
file = {Maliarenko and Mudrak - 2013 - Cactus viruses in fasciated plants.pdf:/Users/alexa/Zotero/storage/27HENZDI/Maliarenko and Mudrak - 2013 - Cactus viruses in fasciated plants.pdf:application/pdf},
issn = {2029-0578, 1392-0146},
journal = {Biologija},
language = {en},
month = nov,
number = {2},
title = {Cactus viruses in fasciated plants},
url = {http://lmaleidykla.lt/ojs/index.php/biologija/article/view/2754},
urldate = {2021-09-03},
volume = {59},
year = {2013},
bdsk-url-1 = {http://lmaleidykla.lt/ojs/index.php/biologija/article/view/2754},
bdsk-url-2 = {https://doi.org/10.6001/biologija.v59i2.2754}}
@book{mahy_desk_2010,
address = {Oxford Heidelberg},
editor = {Mahy, Brian W. J. and Van Regenmortel, Marc H. V.},