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Complete Chloroplast Genome Sequences of Four Species in the Caladium Genus: Comparative and Phylogenetic Analyses

文献类型： 外文期刊

作者： Ye, Yuanjun 1 ; Liu, Jinmei 1 ; Zhou, Yiwei 1 ; Zhu, Genfa 1 ; Tan, Jianjun 1 ; Xu, Yechun 1 ;

作者机构： 1.Guangdong Acad Agr Sci, Environm Hort Res Inst, Guangdong Prov Key Lab Ornamental Plant Germplasm, Guangzhou 510640, Peoples R China

2.Minist Agr, Key Lab Urban Agr South China, Guangzhou 510640, Peoples R China

关键词： Caladium; ornamental foliage plant; chloroplast genome; natural selection pressure; phylogenetic analysis

期刊名称：GENES （ 影响因子：4.141； 五年影响因子：4.474 ）

ISSN：

年卷期： 2022 年 13 卷 12 期

页码：

收录情况： SCI

摘要： Caladiums are promising colorful foliage plants due to their dazzling colors of the leaves, veins, stripes, and patches, which are often cultivated in pots or gardens as decorations. Four wild species, including C. bicolor, C. humboldtii, C. praetermissum, and C. lindenii, were employed in this study, where their chloroplast (cp) genomes were sequenced, assembled, and annotated via high-throughput sequencing. The whole cp genome size ranged from 162,776 bp to 168,888 bp, and the GC contents ranged from 35.09% to 35.91%. Compared with the single large copy (LSC) and single small copy (SSC) regions, more conserved sequences were identified in the inverted repeat regions (IR). We further analyzed the different region borders of nine species of Araceae and found the expansion or contraction of IR/SSC regions might account for the cp genome size variation. Totally, 131 genes were annotated in the cp genomes, including 86 protein-coding genes (PCGs), 37 tRNAs, and eight rRNAs. The effective number of codons (ENC) values and neutrality plot analyses provided the foundation that the natural selection pressure could greatly affect the codon preference. The GC(3) content was significantly lower than that of GC(1) and GC(2), and codons ending with A/U had higher usage preferences. Finally, we conducted phylogenetic relationship analysis based on the chloroplast genomes of twelve species of Araceae, in which C. bicolor and C. humboldtii were grouped together, and C. lindenii was furthest from the other three Caladium species occupying a separate branch. These results will provide a basis for the identification, development, and utilization of Caladium germplasm.

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