Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes

Autor: Prakash Raj Timilsena, Eric K. Wafula, Craig F. Barrett, Saravanaraj Ayyampalayam, Joel R. McNeal, Jeremy D. Rentsch, Michael R. McKain, Karolina Heyduk, Alex Harkess, Matthieu Villegente, John G. Conran, Nicola Illing, Bruno Fogliani, Cécile Ané, J. Chris Pires, Jerrold I. Davis, Wendy B. Zomlefer, Dennis W. Stevenson, Sean W. Graham, Thomas J. Givnish, James Leebens-Mack, Claude W. dePamphilis

Publikováno v: Frontiers in Plant Science, Vol 13 (2022)

We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phyloge

Externí odkaz: https://doaj.org/article/251682fdada7476dab1f51d9b098173d

Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

Autor: Prakash Raj Timilsena, Craig F Barrett, Alma Piñeyro-Nelson, Eric K Wafula, Saravanaraj Ayyampalayam, Joel R McNeal, Tomohisa Yukawa, Thomas J Givnish, Sean W Graham, J Chris Pires, Jerrold I Davis, Cécile Ané, Dennis W Stevenson, Jim Leebens-Mack, Esteban Martínez-Salas, Elena R Álvarez-Buylla, Claude W dePamphilis

Publikováno v: Genome Biology and Evolution. 15

Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although red

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f999c04c93f91932beea6421c69faf1c
https://doi.org/10.1093/gbe/evac183

Phylogenomic analysis of Ranunculales resolves branching events across the order

Autor: Megan M. Augustin, Verónica S. Di Stilio, Toni M. Kutchan, Alastair R. Plant, Claude W. dePamphilis, Jim Leebens-Mack, Saravanaraj Ayyampalayam, Gane Ka-Shu Wong, Amanda Kelly Lane, Stefan Gleissberg

Publikováno v: Botanical Journal of the Linnean Society. 187:157-166

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2c3fac144add0ae8ccac65c9f52efbe6
https://doi.org/10.1093/botlinnean/boy015

Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)

Autor: Saravanaraj Ayyampalayam, Kristian K. Ullrich, Matthew A. Gitzendanner, Chris Bowler, Naim Matasci, Fabio Rocha Jimenez Vieira, Sun Jing, Richard G. Dorrell, Todd J Barkmann, Ling Li, Jim Leebens-Mack, Wensi Du, Gane Ka-Shu Wong, Jun Yu, Eric J. Carpenter, Shuangxiu Wu, Michael S. Barker, Norman J. Wickett

Publikováno v: GigaScience

BackgroundThe 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae).FindingsThis data release accompanies the initiative's final/capstone

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2df792b59c2b93f9fffac218059d7ba7
https://hdl.handle.net/21.11116/0000-0004-ED71-221.11116/0000-0004-ED73-0

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

Autor: Zhen Yue, Chunyan Xu, Mayumi Nakano, Atul Kakrana, John Groenendijk, Ron van der Hulst, Shaochun Luo, Akira Kanno, Saravanaraj Ayyampalayam, Jinsong Zhou, Wenqi Li, Chen Guangyu, Paolo Riccardi, Dave Kudrna, Jeremy N. Ray, Haixin Chen, J. Chris Pires, Helong Chen, Agostino Falavigna, Meizhong Luo, Pierre Lavrijsen, Hongzhi Kong, Jianming Gao, Francesco Mercati, Rod A. Wing, Hongyan Shan, Alex Harkess, Kexian Yi, Blake C. Meyers, Zhang Yueping, Michael R. McKain, Haibao Tang, Siwaret Arikit, Xiangyang Xu, John E. Bowers, Jim Leebens-Mack, Francesco Sunseri, Zichao Mao, Alexa Telgmann-Rauber, Yanling Chen, Sandra M. Mathioni, Yin Ye

Publikováno v: Nature Communications, Vol 8, Iss 1, Pp 1-10 (2017)
Nature communications (2017). doi:10.1038/s41467-017-01064-8
info:cnr-pdr/source/autori:Alex Harkess, Jinsong Zhou, Chunyan Xu, John E. Bowers, Ron Van der Hulst, Saravanaraj Ayyampalayam, Francesco Mercati5, Paolo Riccardi, Michael R. McKain Atul Kakrana, Haibao Tang, Jeremy Ray, John Groenendijk, Siwaret Arikit10, Sandra M. Mathioni Mayumi Nakano, Hongyan Shan, Alexa Telgmann-Rauber, Akira Kanno Zhen Yue, Haixin Chen, Wenqi Li, Yanling Chen, Xiangyang Xu, Yueping Zhang, Shaochun Luo, Helong Chen, Jianming Gao, Zichao Mao, J. Chris Pires, Meizhong Luo, Dave Kudrna, Rod A. Wing, Blake C. Meyers Kexian Yi Hongzhi Kong Pierre Lavrijsen, Francesco Sunseri, Agostino Falavigna Yin Ye James H. Leebens-Mack & Guangyu Chen/titolo:The asparagus genome sheds light on the origin and evolution of a young Y chromosome/doi:10.1038%2Fs41467-017-01064-8/rivista:Nature communications/anno:2017/pagina_da:/pagina_a:/intervallo_pagine:/volume
Harkess, A, Zhou, J, Xu, C, Bowers, J E, van der Hulst, R, Ayyampalayam, S, Mercati, F, Riccardi, P, McKain, M R, Kakrana, A, Tang, H, Ray, J, Groenendijk, J, Arikit, S, Mathioni, S M, Nakano, M, Shan, H, Telgmann-Rauber, A, Kanno, A, Yue, Z, Chen, H, Li, W, Chen, Y, Xu, X, Zhang, Y, Luo, S, Chen, H, Gao, J, Mao, Z, Pires, J C, Luo, M, Kudrna, D, Wing, R A, Meyers, B C, Yi, K, Kong, H, Lavrijsen, P, Sunseri, F, Falavigna, A, Yin, Y, Leebens-Mack, J H & Chen, G 2017, ' The asparagus genome sheds light on the origin and evolution of a young Y chromosome ', Nature Communications, vol. 8, 1279 . https://doi.org/10.1038/s41467-017-01064-8

Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3e42816a1cea6f486c947f9af856d7a1
https://pubmed.ncbi.nlm.nih.gov/29374451