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

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

doi:10.1093/gigascience/giz126

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

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

Research output: Contribution to journal › Article › peer-review

108 Scopus citations

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.

Original language	English (US)
Article number	giz126
Journal	GigaScience
Volume	8
Issue number	10
DOIs	https://doi.org/10.1093/gigascience/giz126
State	Published - Oct 1 2019

Keywords

RNA
assemblies
contamination
genes
plants
transcriptome completeness

ASJC Scopus subject areas

General Medicine

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10.1093/gigascience/giz126

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Carpenter, E. J., Matasci, N., Ayyampalayam, S., Wu, S., Sun, J., Yu, J., Jimenez Vieira, F. R., Bowler, C., Dorrell, R. G., Gitzendanner, M. A., Li, L., Du, W., Ullrich, K., Wickett, N. J., Barkmann, T. J., Barker, M. S., Leebens-Mack, J. H., & Wong, G. K. S. (2019). Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). GigaScience, 8(10), Article giz126. https://doi.org/10.1093/gigascience/giz126

Carpenter, EJ, Matasci, N, Ayyampalayam, S, Wu, S, Sun, J, Yu, J, Jimenez Vieira, FR, Bowler, C, Dorrell, RG, Gitzendanner, MA, Li, L, Du, W, Ullrich, K, Wickett, NJ, Barkmann, TJ, Barker, MS, Leebens-Mack, JH & Wong, GKS 2019, 'Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)', GigaScience, vol. 8, no. 10, giz126. https://doi.org/10.1093/gigascience/giz126

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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.",

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AU - Yu, Jun

AU - Jimenez Vieira, Fabio Rocha

AU - Bowler, Chris

AU - Dorrell, Richard G.

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AU - Ullrich, Kristian

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

Abstract

Keywords

ASJC Scopus subject areas

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