02859nas a2200325   4500000000100000008004100001260001200042653001000054653002600064653000900090653002100099653002100120653002400141653003100165653002300196653001400219653001800233100001600251700001900267700002000286700002000306700001400326700001900340245013900359856007100498300001100569490000700580520193200587022001402519       2021                            d  c12/202110aBUSCO10aplant gene expression10aChia10aexpression atlas10aSalvia Hispanics10aomega-3 fatty acids10apolyunsaturated fatty acid10apseudocereal grain10asuperfood10atranscriptome1 aParul Gupta1 aMatthew Geniza1 aSushma Naithani1 aJeremy Phillips1 aEbaad Haq1 aPankaj Jaiswal00aChia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development.  uhttps://www.frontiersin.org/articles/10.3389/fpls.2021.667678/full  a6676780 v123 a<p>Chia ( L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and development and genetic improvement. We report an RNA-sequencing (RNA-Seq)-based comprehensive transcriptome atlas of Chia sampled from 13 tissue types covering vegetative and reproductive growth stages. We used ~355 million high-quality reads of total ~394 million raw reads from transcriptome sequencing to generate reference transcriptome assembly and the tissue-specific transcript assemblies. After the quality assessment of the merged assemblies and implementing redundancy reduction methods, 82,663 reference transcripts were identified. About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. The assembled transcriptome is estimated to have the complete sequence information for ~86% of the genes found in the Chia genome. Furthermore, the analysis of 53,200 differentially expressed transcripts (DETs) revealed their distinct expression patterns in Chia's vegetative and reproductive tissues; tissue-specific networks and developmental stage-specific networks of transcription factors (TFs); and the regulation of the expression of enzyme-coding genes associated with important metabolic pathways. In addition, we identified 2,411 simple sequence repeats (SSRs) as potential genetic markers from the transcripts. Overall, this study provides a comprehensive transcriptome atlas, and SSRs, contributing to building essential genomic resources to support basic research, genome annotation, functional genomics, and molecular breeding of Chia.</p>
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