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Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides

文献类型： 外文期刊

作者： Gan, Yangying 1 ; Ping, Jingyao 2 ; Liu, Xiaojing 1 ; Peng, Caixia 3 ;

作者机构： 1.Guangdong Acad Agr Sci, Inst Agr Econ & Informat, Key Lab Urban Agr South China, Minist Agr & Rural Affairs, Guangzhou 510640, Peoples R China

2.Sun Yet Sen Univ, Coll Life Sci, Guangzhou 510275, Peoples R China

3.Chinese Acad Sci, Hort Ctr, South China Bot Garden, Guangzhou 510650, Peoples R China

关键词： Miliusa glochidioides plastome; SSRs; Codon usage bias; Phylogenetics

期刊名称：BIOCHEMICAL GENETICS （ 影响因子：2.1； 五年影响因子：2.0 ）

ISSN： 0006-2928

年卷期： 2024 年

页码：

收录情况： SCI

摘要： Annonaceae is the largest family in Magnoliales, exhibiting the greatest diversity among and within genera. In this study, we conducted an analysis of repetitive sequences and codon usage bias in the previously acquired plastome of Miliusa glochidioides. Using a concatenated dataset of shared genes, we constructed the phylogenetic relationships among 27 Annonaceae species. The results showed that the size of the plastomes in the Annonaceae ranged from 159 to 202 kb, with the size of the inverted repeat region ranging from 40 to 65 kb. Within the plastome of M. glochidioides, we identified 42 SSRs, 36 tandem repeats, and 9 dispersed repeats. These SSRs consist of three nucleotide types and eight motif types, with a preference for A/T bases, primarily located in the large single-copy regions and intergenic spacers. Tandem and dispersed repeat sequences were predominantly detected in the IR region. Through codon usage bias analysis, we identified 30 high-frequency codons and 11 optimal codons. The plastome of M. glochidioides demonstrated relatively weak codon usage bias, favoring codons with A/T endings, primarily influenced by natural selection. Phylogenetic analysis revealed that all four subfamilies formed monophyletic groups, with Cananga odorata (Ambavioideae) and Anaxagorea javanica (Anaxagoreoideae) successively nested outside Annonoideae + Malmeoideae. These findings improve our understanding of the plastome of M. glochidioides and provide additional insights for studying plastome evolution in Annonaceae.

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