Phasha Mmatshepho M, Wingfield Brenda D, Coetzee Martin P A, Santana Quentin C, Fourie Gerda, Steenkamp Emma T
Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 South Africa.
Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 South Africa.
G3 (Bethesda). 2017 Nov 6;7(11):3809-3820. doi: 10.1534/g3.117.300344.
Removal of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs) have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspects of intron structure and diversity are taxon-specific, which can complicate the accuracy of gene prediction methods. Using core genes, we evaluated the distribution and architecture of spliceosomal introns, and linked these characteristics to the accuracy of the predicted gene models of the genome of this fungus. We also evaluated intron distribution and architecture in , , and , and made comparisons with Results indicated that and the three other species have canonical 5' and 3' splice sites, but with subtle differences that are apparently not shared with those of other fungal genera. The polypyrimidine tract of introns was also found to be highly divergent among species and genes. Furthermore, the conserved adenosine nucleoside required during the first step of splicing is contained within unique branch site motifs in certain introns. Data generated here show that introns of , as well as , , and , are characterized by a number of unique features such as the CTHAH and ACCAT motifs of the branch site. Incorporation of such information into genome annotation software will undoubtedly improve the accuracy of gene prediction methods used for species and related fungi.
从转录的RNA中去除内含子是真核生物中mRNA产生过程中的关键步骤。现有的全基因组序列和表达序列标签（EST）增加了我们对这一过程的了解，并揭示了真核生物之间的各种共性。然而，内含子结构和多样性的某些方面是特定于分类群的，这可能会使基因预测方法的准确性变得复杂。我们使用核心基因评估了剪接体内含子的分布和结构，并将这些特征与该真菌基因组预测基因模型的准确性联系起来。我们还评估了[具体物种1]、[具体物种2]和[具体物种3]中的内含子分布和结构，并与[对比物种]进行了比较。结果表明，[具体物种1]和其他三个物种具有典型的5'和3'剪接位点，但存在细微差异，这些差异显然与其他真菌属不同。还发现[具体物种1]内含子的多嘧啶序列在物种和基因之间也高度不同。此外，剪接第一步所需的保守腺苷核苷包含在某些[具体物种1]内含子独特的分支位点基序中。此处生成的数据表明，[具体物种1]以及[具体物种2]、[具体物种3]和[对比物种]的内含子具有许多独特特征，如分支位点的CTHAH和ACCAT基序。将这些信息纳入基因组注释软件无疑将提高用于[具体物种1]及相关真菌的基因预测方法的准确性。
