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

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

Eric J Carpenter  1 , Naim Matasci  2 , Saravanaraj Ayyampalayam  3 , Shuangxiu Wu  4 , Jing Sun  4 , Jun Yu  4 , Fabio Rocha Jimenez Vieira  5 , Chris Bowler  5 , Richard G Dorrell  5 , Matthew A Gitzendanner  6 , Ling Li  7 , Wensi Du  7 , Kristian K Ullrich  8 , Norman J Wickett  9   10 , Todd J Barkmann  11 , Michael S Barker  12 , James H Leebens-Mack  13 , Gane Ka-Shu Wong  1   7   14
Affiliations

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

Eric J Carpenter et al. Gigascience. .

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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Figures

Figure 1:
Figure 1:
A, Overview of the total sequence percentage verified to be of contaminant origin (red), or inferred to be possible contaminants in other sequence libraries (grey) in all 1KP libraries, and libraries inferred to be contaminated through the 18S phylogenetic placement. B, 21 libraries in which >6% of the total sequences are potential contaminants. C, Heat map of inferred contaminant interactions between pairs of species; contaminated species are shown on the vertical axis and contaminating species on the horizontal axis.
Figure 2:
Figure 2:
Fraction of the gene sets found (complete + fragments) vs the number of scaffolds (≥300 bp) in the assemblies. For each sample, the fractions of the eukaryota and embryophyta sets found in the assemblies are calculated with BUSCO and the fraction of the CEGMA 248 set with the CRBB tool. All 3 sets are more completely recovered at higher scaffold counts, but the BUSCO embryophyta set is less complete in our samples.
See this image and copyright information in PMC

References

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