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Gigascience. 2019 Oct 1;8(10). pii: giz126. doi: 10.1093/gigascience/giz126.

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

Author information

1
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
2
CyVerse, University of Arizona, AZ,1657 East Helen St, Tucson AZ, USA 85721 USA.
3
Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA 30602, US.
4
CAS Key Laboratory of Genome Sciences and Information, Beijing, Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
5
Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.
6
Department of Biology, University of Florida, Gainesville, FL 32611, USA.
7
BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
8
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
9
Chicago Botanic Garden, Glencoe, IL 60022.
10
Program in Biological Sciences, Northwestern University, Evanston, IL 60208, USA.
11
Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008-5410, USA.
12
Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
13
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
14
Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada.

Abstract

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.

KEYWORDS:

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

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