Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
Planta. 2019 Apr;249(4):1133-1142. doi: 10.1007/s00425-018-03073-3. Epub 2019 Jan 2.
Alternative splicing EVENTS were genome-wide identified for four legume species, and nitrogen fixation-related gene families and evolutionary analysis was also performed. Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. Investigation of the genome-wide conserved AS events across different species will help with the understanding of the evolution of the functional diversity in legumes, allowing for genetic improvement. Genome-wide identification and characterization of AS were performed using the publically available mRNA, EST, and RNA-Seq data for four important legume species. A total of 15,165 AS genes in Glycine max, 6077 in Cicer arietinum, 7240 in Medicago truncatula, and 7358 in Lotus japonicus were identified. Intron retention (IntronR) was the dominant AS type among the identified events, with IntronR occurring from 53.76% in M. truncatula to 43.91% in C. arietinum. We identified 1159 AS genes that were conserved among four species. Furthermore, nine nitrogen fixation-related gene families with 237 genes were identified, and 80 of them were AS, accounting for the 43.48% in G. max and 27.78% in C. arietinum. An evolutionary analysis showed that these AS genes tended to be located adjacent to each other in the evolutionary tree and are unbalanced in the distribution in the sub-family. This study provides a foundation for future studies on transcription complexity, evolution, and the role of AS on plant functional regulation.
对四种豆科植物进行了全基因组的可变剪接事件鉴定，并进行了固氮相关基因家族的进化分析。可变剪接（AS）是一种关键的调控机制，有助于转录组和蛋白质组的多样性。研究不同物种间全基因组保守的 AS 事件有助于理解豆科植物功能多样性的进化，从而实现遗传改良。使用四种重要豆科植物的公共 mRNA、EST 和 RNA-Seq 数据，对 AS 进行了全基因组鉴定和特征分析。在 Glycine max 中鉴定到了 15165 个 AS 基因，在 Cicer arietinum 中鉴定到了 6077 个，在 Medicago truncatula 中鉴定到了 7240 个，在 Lotus japonicus 中鉴定到了 7358 个。内含子保留（IntronR）是鉴定事件中主要的 AS 类型，在鉴定到的事件中，IntronR 从 M. truncatula 的 53.76%到 C. arietinum 的 43.91%。我们鉴定到了 1159 个在四个物种中保守的 AS 基因。此外，还鉴定到了 9 个与固氮相关的基因家族，共 237 个基因，其中 80 个是 AS，占 G. max 的 43.48%和 C. arietinum 的 27.78%。进化分析表明，这些 AS 基因在进化树上倾向于彼此相邻，并且在亚家族中的分布不平衡。这项研究为进一步研究转录复杂性、进化以及 AS 在植物功能调控中的作用提供了基础。
