Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae)
Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae)
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DOI：
10.1016/j.ygeno.2020.01.006
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发表时间：
2020-05-01
期刊：
影响因子：
4.4
通讯作者：
McKain, Michael R.
中科院分区：
文献类型：
--
作者：
Henriquez, Claudia L.;Abdullah;McKain, Michael R.
天南星亚科是天南星科中最大和最多样化的亚科。尽管其农业和园艺的重要性，基因组资源是稀疏的这个亚科。在这里，我们报告从头组装和充分注释的叶绿体基因组的13 Aroideae物种。四分叶绿体基因组（大小范围为158，177 - 170，037 bp）由一个大的单拷贝（LSC; 75，594 - 94，702 bp）、一个小的单拷贝（SSC; 12，903 - 23，981 bp）和一对反向重复序列（IR; 25，266 - 34，840 bp）组成。显着的基因重排和IRs收缩/扩张被发现为和马蹄莲aethiopica。密码子使用，氨基酸频率，寡核苷酸重复，GC含量和基因特征显示13种之间的相似性。寡核苷酸重复序列的数目与物种的基因组大小或系统发育位置无关。系统发育分析证实了Aroideae的单系性，但无法解决的马蹄莲和舌的位置。
Aroideae is the largest and most diverse subfamily of the plant family Araceae. Despite its agricultural and horticultural importance, the genomic resources are sparse for this subfamily. Here, we report de novo assembled and fully annotated chloroplast genomes of 13 Aroideae species. The quadripartite chloroplast genomes (size range of 158,177-170,037 bp) are comprised of a large single copy (LSC; 75,594-94,702 bp), a small single copy (SSC; 12,903-23,981 bp) and a pair of inverted repeats (IRs; 25,266-34,840 bp). Notable gene rearrangements and IRs contraction / expansions were found for Anchomanes hookeri and Zantedeschia aethiopica. Codon usage, amino acid frequencies, oligonucleotide repeats, GC contents, and gene features revealed similarities among the 13 species. The number of oligonucleotide repeats was uncorrelated with genome size or phylogenetic position of the species. Phylogenetic analyses corroborated the monophyly of Aroideae but were unable to resolve the positions of Calla and Schismatoglottis.