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油菜（十字花科）中一个温敏雄性不育突变体的从头转录组重建

De novo transcriptome reconstruction of a thermo-sensitive male sterility mutant in rapeseed (; Brassicaceae).

作者信息

Liu Xi-Qiong, Yu Cheng-Yu, Dong Jun-Gang, Xu Ai-Xia, Hu Sheng-Wu

机构信息

College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, People's Republic of China.

出版信息

Appl Plant Sci. 2017 Dec 22;5(12). doi: 10.3732/apps.1700077. eCollection 2017 Dec.

DOI:10.3732/apps.1700077
PMID:29299393
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5749817/
Abstract

PREMISE OF THE STUDY

SP2S is a spontaneous thermo-sensitive genic male sterility (TGMS) mutation that facilitates two-line hybrid breeding in (Brassicaceae). De novo assembly of the floral bud transcriptome of SP2S can provide a foundation for deciphering the transcriptional regulation of SP2S in response to temperature change.

METHODS

mRNAs of the young floral buds of SP2S and its near-isogenic line SP2F grown under cool (16°C)/warm (22°C) conditions were sequenced on an Illumina Solexa platform, producing 239.7 million short reads with a total length of 19.95 Gbp.

RESULTS

The reads were assembled de novo using the Trinity program, resulting in 135,702 transcripts with an average length of 784 bp, an N50 value of 1221 bp, and a total length of 107 Mbp. We identified 24,157 cDNA-derived simple sequence repeats in the assembly. We found 137 and 195 single-nucleotide polymorphisms and 49 and 51 differentially regulated KEGG orthology groups when comparing sample SP2S at 22°C vs. SP2S at 16°C and sample SP2S at 22°C vs. SP2F at 22°C, respectively.

DISCUSSION

The numerous differentially expressed genes and the derived single-nucleotide polymorphisms show abnormal transcriptional regulation in the TGMS system. These results outline an intricate transcriptional regulation that occurred in the rapeseed TGMS SP2S when the temperature changed.

摘要

研究前提

SP2S是一种自发的温敏雄性不育（TGMS）突变体，有助于十字花科的两系杂交育种。对SP2S花芽转录组进行从头组装可为解析SP2S响应温度变化的转录调控提供基础。

方法

在Illumina Solexa平台上对在低温（16°C）/高温（22°C）条件下生长的SP2S及其近等基因系SP2F的幼嫩花芽mRNA进行测序，产生了2.397亿条短读段，总长度为19.95 Gbp。

结果

使用Trinity程序对读段进行从头组装，得到135,702个转录本，平均长度为784 bp，N50值为1221 bp，总长度为107 Mbp。我们在组装中鉴定出24,157个cDNA衍生的简单序列重复。分别比较22°C下的样本SP2S与16°C下的SP2S以及22°C下的样本SP2S与22°C下的SP2F时，我们发现了137和195个单核苷酸多态性以及49和51个差异调节的KEGG直系同源组。

讨论

众多差异表达基因和衍生的单核苷酸多态性表明TGMS系统中存在异常转录调控。这些结果概述了油菜TGMS SP2S在温度变化时发生的复杂转录调控。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/415dac481d5b/apps.1700077fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/11ca7a271b7f/apps.1700077fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/6da887accbd6/apps.1700077fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/194d21d98cf7/apps.1700077fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/2afa4db23fdb/apps.1700077fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/e9c7e830cece/apps.1700077fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/c7faf94b4821/apps.1700077fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/415dac481d5b/apps.1700077fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/11ca7a271b7f/apps.1700077fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/6da887accbd6/apps.1700077fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/194d21d98cf7/apps.1700077fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/2afa4db23fdb/apps.1700077fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/e9c7e830cece/apps.1700077fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/c7faf94b4821/apps.1700077fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b659/5749817/415dac481d5b/apps.1700077fig7.jpg

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