Jiang Jinjin, Wang Yue, Zhu Bao, Fang Tingting, Fang Yujie, Wang Youping
Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
BMC Plant Biol. 2015 Jan 27;15:22. doi: 10.1186/s12870-015-0417-5.
Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale.
We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species.
Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.
芸苔属包含许多通过祖先基因组三倍化或两个二倍体祖先杂交而成功培育的多倍体起源作物物种，具有复杂的重复序列和转座子。由三个二倍体和三个双二倍体组成的U三角对于分析多倍化后的复杂基因组是最优的。新一代测序技术能够在全球范围内对多倍体进行转录组分析。
我们通过数字基因表达分析研究了三个二倍体（白菜、黑芥和甘蓝）和三个双二倍体（甘蓝型油菜、芥菜型油菜和埃塞俄比亚芥）的基因表达模式。总共，文库产生了570万至610万条原始读数，每个文库的干净标签被映射到白菜基因组的18547 - 21995个基因上。对文库中明确标签映射的基因进行了比较。此外，还在二倍体之间以及二倍体与双二倍体之间探索了大多数差异表达基因（DEG）。进行了基因本体分析，以便将这些DEG功能分类到不同类别中。进行了京都基因与基因组百科全书分析，以便将这些DEG分配到大约120条途径中。其中，代谢途径、次生代谢物生物合成途径和过氧化物酶体途径得到了富集。对芸苔属双二倍体中的非加性基因进行了分析，结果表明多倍体中的直系同源基因经常以非加性模式表达。甲基转移酶基因在芸苔属物种中表现出差异表达模式。
我们的结果提供了对天然芸苔属物种转录组复杂性的理解。二倍体和异源多倍体中的基因表达变化可能有助于阐明芸苔属物种之间的形态和生理差异。
