A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

Abstract

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relativesThe International Center for Tropical Agriculture (CIAT) believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture.CIAT is committed to creating and sharing knowledge and information openly and globally. We do this through collaborative research as well as through the open sharing of our data, tools, and publications. Citation:Sarah For more information, please contact CIAT Library at CIAT-Library@cgiar.org. Accepted ArticleThis article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1755-0998.12587 This article is protected by copyright. All rights reserved. Accepted ArticleThis article is protected by copyright. All rights reserved. AbstractWe produced a unique large dataset of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11eudicots. All contigs were annotated using BLAST, prot4EST, and Blast2GO. A strong originality of the dataset is that each crop is associated with close relative species, which will permit whole genome comparative evolutionary studies between crops and their wild related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at

Evolutionary forces affecting synonymous variations in plant genomes

“…When a well-annotated reference genome was available (see Material and methods), we used it as a reference for read mapping. Otherwise we used a de novo transcriptome assembly already obtained for these species (focal + outgroups) [48] (Table 1 and S2 Table). After quality trimming and mapping of the raw reads, we kept contigs with at least one read mapped for every individual, giving between more than 24,000 (P. glaucum) and 45,000 (in O. europaea) contigs per species (Table 1).…”

“…A phylogeny of these species is shown in Fig 1. For practical reasons, we chose diploid cultivated species but focused our analysis on wild populations except in Elaeis guineensis where domestication is very recent and limited (19 th century [45]). Using the same methodology as [48], we sequenced for each species the transcriptome of ten individuals (12 in the case of C. canephora and V. vinifera, nine in the case of S. bicolor and five in the case of D. abyssinica) plus two individuals coming from two outgroup species, using RNA-seq (see S3 Text for details). After quality cleaning, reads were either mapped on the transcriptome extracted from the reference genome (when available, see Table 1) or on the de novo transcriptome of each species (including outgroups) obtained from [48].…”

“…Using the same methodology as [48], we sequenced for each species the transcriptome of ten individuals (12 in the case of C. canephora and V. vinifera, nine in the case of S. bicolor and five in the case of D. abyssinica) plus two individuals coming from two outgroup species, using RNA-seq (see S3 Text for details). After quality cleaning, reads were either mapped on the transcriptome extracted from the reference genome (when available, see Table 1) or on the de novo transcriptome of each species (including outgroups) obtained from [48]. For C. canephora and its outgroups, no transcriptome was available.…”

“…For C. canephora and its outgroups, no transcriptome was available. We thus applied the same methodology and pipeline as in [48] to assemble and annotate contigs. For banana, M. acuminata, Robusta coffee tree, C. canephora, and for the outgroup Phoenix dactylifera, genome sequences were available but the quality of mapping was not optimal because of problems of definition of exon/intron boundaries.…”

Domestication and Genetics of Papaya: A Review

“…For instance, the functional genomics aspects of domestication will help assess how many and which genes show differences in expression between wild and domesticated types (Sarah et al, 2017), which factors affect gene expression, and a better understanding of biotic interactions and how these have affected crop evolution, among many others (Gepts, 2014).…”