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

BACKGROUND: The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae). FINDINGS: This data release accompanies the initiative's final/capstone publication on a set of 3 analyses infer...

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Autores principales: Carpenter, Eric J, Matasci, Naim, Ayyampalayam, Saravanaraj, Wu, Shuangxiu, Sun, Jing, Yu, Jun, Jimenez Vieira, Fabio Rocha, Bowler, Chris, Dorrell, Richard G, Gitzendanner, Matthew A, Li, Ling, Du, Wensi, K. Ullrich, Kristian, Wickett, Norman J, Barkmann, Todd J, Barker, Michael S, Leebens-Mack, James H, Wong, Gane Ka-Shu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6808545/
https://www.ncbi.nlm.nih.gov/pubmed/31644802
http://dx.doi.org/10.1093/gigascience/giz126
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author Carpenter, Eric J
Matasci, Naim
Ayyampalayam, Saravanaraj
Wu, Shuangxiu
Sun, Jing
Yu, Jun
Jimenez Vieira, Fabio Rocha
Bowler, Chris
Dorrell, Richard G
Gitzendanner, Matthew A
Li, Ling
Du, Wensi
K. Ullrich, Kristian
Wickett, Norman J
Barkmann, Todd J
Barker, Michael S
Leebens-Mack, James H
Wong, Gane Ka-Shu
author_facet Carpenter, Eric J
Matasci, Naim
Ayyampalayam, Saravanaraj
Wu, Shuangxiu
Sun, Jing
Yu, Jun
Jimenez Vieira, Fabio Rocha
Bowler, Chris
Dorrell, Richard G
Gitzendanner, Matthew A
Li, Ling
Du, Wensi
K. Ullrich, Kristian
Wickett, Norman J
Barkmann, Todd J
Barker, Michael S
Leebens-Mack, James H
Wong, Gane Ka-Shu
author_sort Carpenter, Eric J
collection PubMed
description BACKGROUND: The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae). FINDINGS: This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations. CONCLUSIONS: These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages.
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spelling pubmed-68085452019-10-28 Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP) Carpenter, Eric J Matasci, Naim Ayyampalayam, Saravanaraj Wu, Shuangxiu Sun, Jing Yu, Jun Jimenez Vieira, Fabio Rocha Bowler, Chris Dorrell, Richard G Gitzendanner, Matthew A Li, Ling Du, Wensi K. Ullrich, Kristian Wickett, Norman J Barkmann, Todd J Barker, Michael S Leebens-Mack, James H Wong, Gane Ka-Shu Gigascience Data Note BACKGROUND: The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae). FINDINGS: This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations. CONCLUSIONS: These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages. Oxford University Press 2019-10-23 /pmc/articles/PMC6808545/ /pubmed/31644802 http://dx.doi.org/10.1093/gigascience/giz126 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Carpenter, Eric J
Matasci, Naim
Ayyampalayam, Saravanaraj
Wu, Shuangxiu
Sun, Jing
Yu, Jun
Jimenez Vieira, Fabio Rocha
Bowler, Chris
Dorrell, Richard G
Gitzendanner, Matthew A
Li, Ling
Du, Wensi
K. Ullrich, Kristian
Wickett, Norman J
Barkmann, Todd J
Barker, Michael S
Leebens-Mack, James H
Wong, Gane Ka-Shu
Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)
title Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)
title_full Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)
title_fullStr Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)
title_full_unstemmed Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)
title_short Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)
title_sort access to rna-sequencing data from 1,173 plant species: the 1000 plant transcriptomes initiative (1kp)
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6808545/
https://www.ncbi.nlm.nih.gov/pubmed/31644802
http://dx.doi.org/10.1093/gigascience/giz126
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