Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.
Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.
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芸苔属二倍体和异源多倍体内基因表达差异的数字基因表达分析
DOI：
10.1186/s12870-015-0417-5
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发表时间：
2015-01-27
影响因子：
5.3
通讯作者：
Wang Y
中科院分区：
文献类型：
--
作者：
Jiang J;Wang Y;Zhu B;Fang T;Fang Y;Wang Y
Brassica包括许多成功培育的多倍体作物物种，通过祖先基因组三倍体或两个二倍体后代之间的杂交，显示出复杂的重复序列和转座子。U三角由三个二倍体和三个双二倍体组成，最适合分析多倍化后的复杂基因组。下一代测序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(甘蓝型油菜、黑甘蓝和甘蓝)和三个双二倍体(甘蓝型油菜、芥菜型油菜和隆突甘蓝型油菜)的基因表达模式。总共，这些文库产生了570万到610万个原始读数，每个文库的干净标签被映射到白菜基因组的18547-21995个基因。对文库中明确标记的基因进行了比较。此外，大多数差异表达基因(Deg)在二倍体之间以及在二倍体和双二倍体之间也被发现。进行基因本体论分析，从功能上将这些deg分为不同的类别。通过京都百科全书的基因和基因组分析，将这些基因划分为大约120条途径，其中代谢途径、次生代谢物的生物合成和过氧化物体途径都得到了丰富。对甘蓝型双二倍体中的非加性基因进行了分析，结果表明，多倍体中的同源基因经常以非加性的方式表达。甲基转移酶基因在十字花科植物中表现出差异表达模式。我们的结果为了解天然油菜物种的转录组复杂性提供了依据。二倍体和异源多倍体中基因表达的变化可能有助于阐明油菜属植物之间的形态和生理差异。本文的在线版本(doi：10.1186/s12870-0150417-5)包含补充材料，授权用户可以使用。
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. The online version of this article (doi:10.1186/s12870-015-0417-5) contains supplementary material, which is available to authorized users.
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影响因子：
4.3
作者：
Batista, Catia;Barros, Lillian;Ferreira, Isabel C. F. R.
通讯作者：
Ferreira, Isabel C. F. R.
影响因子：
7
作者：
Lysak, MA;Koch, MA;Schubert, I
通讯作者：
Schubert, I
新合成甘蓝型油菜异源四倍体及其早期代的蛋白质组变化
影响因子：
2.1
作者：
Kong, Fang;Mao, Shanjing;Wang, Youping
通讯作者：
Wang, Youping
影响因子：
4.4
作者：
Higgins J;Magusin A;Trick M;Fraser F;Bancroft I
通讯作者：
Bancroft I
影响因子：
5.8
作者：
Conesa, A;Götz, S;Robles, M
通讯作者：
Robles, M