Kamra Kashish, Jung Joonhyung, Kim Joo-Hwan
Department of Life Sciences, Gachon University, Seongnam, Gyeonggi, Republic of Korea.
Front Plant Sci. 2023 Jan 31;14:1066708. doi: 10.3389/fpls.2023.1066708. eCollection 2023.
The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies-Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae-which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated () the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that and were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies-Crocoideae, Nivenioideae, and Aristeoideae-shared a common 2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of within the tribal classification of the subfamily Crocoideae.
质体基因组已被证明是研究植物系统发育中深层关联的有效工具，这归因于其高度保守的结构、单亲遗传以及进化速率的有限变异。鸢尾科包含2000多个物种，包括许多具有重要经济意义的类群，这些类群经常用于食品工业、医药以及观赏和园艺用途。对叶绿体DNA的分子研究已证实该科在天门冬目非天门冬类群中的位置。鸢尾科目前的亚科分类承认七个亚科——异苞鸢尾亚科、尼维鸢尾亚科、鸢尾亚科、番红花亚科、地鸢尾科、芒苞鸢尾亚科和澳鸢尾亚科——这些亚科得到了有限的质体DNA区域的支持。迄今为止，尚未对鸢尾科进行比较系统基因组学研究。我们组装并注释了24个类群的质体基因组，以及代表鸢尾科所有七个亚科的七个已发表物种，并使用Illumina MiSeq平台进行了比较基因组学研究。自养鸢尾科的质体基因组包含79个蛋白质编码基因、30个tRNA基因和4个rRNA基因，长度在150,062至164,622 bp之间。基于最大简约法、最大似然法和贝叶斯推断分析对质体基因组序列进行的系统发育分析表明，[物种名称1]和[物种名称2]关系密切，得到了较强支持值的支持，这与最近的系统发育研究有很大差异。此外，我们在一些物种中发现了基因组事件，如序列倒位、缺失、突变和假基因化。此外，在七个质体基因组区域发现了最大的核苷酸变异性，可用于未来的系统发育研究。值得注意的是，三个亚科——番红花亚科、尼维鸢尾亚科和芒苞鸢尾亚科——共享一个共同的2个基因座缺失。我们的研究是对鸢尾科7/7个亚科和9/10个族的完整质体基因组进行比较研究的初步报告，阐明了其结构特征，并揭示了鸢尾科内质体基因组的进化和系统发育关系。此外，需要进一步研究以更新[物种名称3]在番红花亚科族分类中的相对位置。
