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

被引：116

作者：

Carpenter, Eric J. ^{[1
]}

Matasci, Naim ^{[2
,3
]}

Ayyampalayam, Saravanaraj ^{[4
]}

Wu, Shuangxiu ^{[5
]}

Sun, Jing ^{[5
]}

Yu, Jun ^{[5
]}

Vieira, Fabio Rocha Jimenez ^{[6
]}

Bowler, Chris ^{[6
]}

Dorrell, Richard G. ^{[6
]}

Gitzendanner, Matthew A. ^{[7
]}

Li, Ling ^{[8
]}

Du, Wensi ^{[8
]}

Ullrich, Kristian K. ^{[9
]}

Wickett, Norman J. ^{[10
,11
]}

Barkmann, Todd J. ^{[12
]}

Barker, Michael S. ^{[13
]}

Leebens-Mack, James H. ^{[14
]}

Wong, Gane Ka-Shu ^{[15
]}

机构：

[1] Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada

[2] Univ Arizona, CyVerse, 1657 East Helen St, Tucson, AZ 85721 USA

[3] Univ Southern Calif, Lawrence J Ellison Inst Transformat Med, Los Angeles, CA 90033 USA

[4] Univ Georgia, Georgia Adv Comp Resource Ctr, Athens, GA 30602 USA

[5] Chinese Acad Sci, Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100101, Peoples R China

[6] Univ PSL, INSERM, CNRS, IBENS,Dept Biol,Ecole Normale Super, F-75005 Paris, France

[7] Univ Florida, Dept Biol, Gainesville, FL 32611 USA

[8] BGI Shenzhen, Shenzhen 518083, Guangdong, Peoples R China

[9] Max Planck Inst Evolutionary Biol, Dept Evolutionary Genet, Plon, Germany

[10] Chicago Bot Garden, Glencoe, IL 60022 USA

[11] Northwestern Univ, Program Biol Sci, Evanston, IL 60208 USA

[12] Western Michigan Univ, Dept Biol Sci, Kalamazoo, MI 49008 USA

[13] Univ Arizona, Dept Ecol Evolutionary Biol, Tucson, AZ 85721 USA

[14] Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA

[15] Univ Alberta, Dept Med, Edmonton, AB T6G 2E1, Canada

来源：

GIGASCIENCE | 2019年 / 8卷 / 10期

关键词：

RNA; plants; assemblies; genes; contamination; transcriptome completeness;

D O I：

10.1093/gigascience/giz126

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

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