Singh Kaushal Pratap, Kumari Preetesh, Yadava Devendra Kumar
ICAR-Directorate of Rapeseed Mustard Research, Bharatpur, India.
Genetics Division, ICAR-Indian Agricultural Research Institute, New Delhi, India.
Front Genet. 2022 Sep 16;13:958217. doi: 10.3389/fgene.2022.958217. eCollection 2022.
Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion ( + ), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2 = 60) was produced and used for transcriptome analysis to uncover genes for thermotolerance, annotations, and microsatellite markers for future molecular breeding. Illumina Novaseq 6000 generated a total of 76,055,546 paired-end raw reads, which were used for assembly, resulting in the development of 486,066 transcripts. A total of 133,167 coding sequences (CDSs) were predicted from transcripts with a mean length of 507.12 bp and 46.15% GC content. The BLASTX search of CDSs against public protein databases showed a maximum of 126,131 (94.72%) and a minimum of 29,810 (22.39%) positive hits. Furthermore, 953,773 gene ontology (GO) terms were found in 77,613 (58.28%) CDSs, which were divided into biological processes (49.06%), cellular components (31.67%), and molecular functions (19.27%). CDSs were assigned to 144 pathways by a pathway study using the KEGG database and 1,551 pathways by a similar analysis using the Reactome database. Further investigation led to the discovery of genes encoding over 2,000 heat shock proteins (HSPs). The discovery of a large number of HSPs in allohexaploid Brassica validated our earlier findings for heat tolerance at seed maturity. A total of 15,736 SSRs have been found in 13,595 CDSs, with an average of one SSR per 4.29 kb length and an SSR frequency of 11.82%. The first transcriptome assembly of a meiotically stable allohexaploid Brassica has been given in this article, along with functional annotations and the presence of SSRs, which could aid future genetic and genomic studies.
作物甘蓝型油菜包含单基因组和双基因组物种，自然界中没有三基因组甘蓝型油菜的证据。通过体细胞融合（+），产生了一种新型的异源六倍体三基因组甘蓝型油菜（H1 = AABBSS；2n = 60），并用于转录组分析，以发现耐热性基因、注释以及用于未来分子育种的微卫星标记。Illumina Novaseq 6000共产生了76,055,546对末端原始读数，用于组装，从而产生了486,066个转录本。从转录本中预测出总共133,167个编码序列（CDS），平均长度为507.12 bp，GC含量为46.15%。将CDS与公共蛋白质数据库进行BLASTX搜索，显示最多有126,131个（94.72%）阳性匹配，最少有29,810个（22.39%）阳性匹配。此外，在77,613个（58.28%）CDS中发现了953,773个基因本体论（GO）术语，这些术语分为生物过程（49.06%）、细胞成分（31.67%）和分子功能（19.27%）。通过使用KEGG数据库的通路研究，CDS被分配到144条通路，通过使用Reactome数据库的类似分析，CDS被分配到1,551条通路。进一步的研究发现了编码超过2000种热休克蛋白（HSP）的基因。在异源六倍体甘蓝型油菜中发现大量HSP证实了我们早期关于种子成熟时耐热性的发现。在13,595个CDS中总共发现了15,736个SSR，平均每4.29 kb长度有一个SSR，SSR频率为11.82%。本文给出了减数分裂稳定的异源六倍体甘蓝型油菜的首个转录组组装结果，以及功能注释和SSR的存在情况，这有助于未来的遗传和基因组研究。
