High-throughput sequencing reveals single nucleotide variants in long... - SRA

SRX1818514: High-throughput sequencing reveals single nucleotide variants in longer kernel bread wheat
1 ILLUMINA (Illumina HiSeq 2000) run: 82,840 spots, 72.9M bases, 19.4Mb downloads

Design: Grains were collected at different developmental stages from both lines at 7, 14, 21, 28, and 35 days after flowering, and mature seeds (deposited for one year, acting as the original day); pooled samples were obtained by mixing ten grains from each wheat strain at each developmental stage mentioned above; these samples were used for the generation of small RNA libraries of Yunong 201 and 3114. Mixing all the sequences in diverse days acted as the last fasta sequence for 201 and 3114,respectely.

Submitted by: Henan Agricultural University

Study: High-throughput sequencing reveals single nucleotide variants in longer kernel bread wheat

PRJNA324305 • SRP076067 • All experiments • All runs

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The transcriptomes of bread wheat Yunong 201 and its ethyl methanesulfonate (EMS) derivative Yunong 3114 were obtained by next-sequencing technology. Single nucleotide variants (SNVs) in the wheat strains were explored and compared. A total of 5907 and 6287 nonsynonymous SNVs were acquired for Yunong 201 and 3114, respectively. The total GC content of Yunong 201 was higher than that of Yunong 3114, because EMS preferentially acts on GC residues. A total of 4021 genes with SNVs were obtained. The genes that underwent nonsynonymous SNVs were significantly involved in ATP binding, protein phosphorylation, and cellular protein metabolic process. The heat map analysis also indicated that most of these mutant genes were significantly differentially expressed at different developmental stages. The SNVs in these genes possibly contribute to the longer kernel length of Yunong 3114. Our data provide useful information on wheat transcriptome for future studies on wheat functional genomics. This study could also help in illustrating the gene functions of the nonsynonymous SNVs of Yunong 201 and 3114.

Sample: wheat yunong 3114

SAMN05200530 • SRS1481106 • All experiments • All runs

Organism: Triticum aestivum

Library:

Name: yunong 201

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: unspecified

Layout: PAIRED

Runs: 1 run, 82,840 spots, 72.9M bases, 19.4Mb

Run	# of Spots	# of Bases	Size	Published
SRR3623313	82,840	72.9M	19.4Mb	2017-10-08

ID:: 2599377

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