Cargando…
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...
Autores principales: | , , , , , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1783461772102991872 |
---|---|
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. |
format | Online Article Text |
id | pubmed-6808545 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT carpenterericj accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT matascinaim accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT ayyampalayamsaravanaraj accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT wushuangxiu accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT sunjing accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT yujun accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT jimenezvieirafabiorocha accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT bowlerchris accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT dorrellrichardg accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT gitzendannermatthewa accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT liling accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT duwensi accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT kullrichkristian accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT wickettnormanj accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT barkmanntoddj accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT barkermichaels accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT leebensmackjamesh accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp AT wongganekashu accesstornasequencingdatafrom1173plantspeciesthe1000planttranscriptomesinitiative1kp |