Jung Joonhyung, Kim Changkyun, Kim Joo-Hwan
Department of Life Sciences, Gachon University, 1342 Seongnamdaero, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
Plant Research Division, Honam National Institute of Biological Resources, 99 Gohadoan-gil, Mokpo-si, Jeollanam-do, 58762, Republic of Korea.
BMC Genomics. 2021 Apr 2;22(1):231. doi: 10.1186/s12864-021-07541-1.
Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time.
All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes.
In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.
鸭跖草科（鸭跖草目）包含41个属，广泛分布于东半球和西半球，但欧洲除外。该科属间关系已在多项形态学和分子研究中有所提及。然而，由于形态变异大且支持值低，难以解释它们之间的关系。目前，许多研究人员一直在使用完整的叶绿体基因组数据来推断陆地植物的进化。在本研究中，我们使用Mi-seq平台完成了15个鸭跖草亚科新的质体基因组序列。我们首次利用基因组数据揭示结构变异并重建属的疑难位置。
所有检测的鸭跖草亚科物种都有三个假基因（accD、rpoA和ycf15），前两个可能是鸭跖草目中的一个共衍征。鸭跖草族中只有四个物种出现了IR扩展，这影响了rpl22基因的重复。我们在四个类群（穿鞘花属、水竹叶属、水苋菜属和竹叶吉祥草属）中鉴定出长度约为3至15 kb的倒位。使用77个叶绿体蛋白编码基因进行的最大简约法、最大似然法和贝叶斯推断的系统发育分析表明，苞叶鸭跖草属与鸭跖草族关系最为密切，支持值很高。这一结果与鸭跖草科目前的分类有显著差异。此外，我们解决了竹叶吉祥草亚科位置不明确以及二室花亚科单系性的问题。在十个具有高核苷酸多样性值（Pi > 0.045）且长度超过500 bp的编码序列（ndhH、rpoC2、ndhA、rps3、ndhG、ndhD、ccsA、ndhF、matK和ycf1）中，四个编码序列（ndhH、rpoC2、matK和ycf1）表明它们与从77个叶绿体蛋白编码基因推导的拓扑结构一致。
在本研究中，我们提供了鸭跖草亚科类群15个完整质体基因组的详细信息。我们鉴定出了特征性假基因和核苷酸多样性，可用于推断该科进化历史。此外，需要进一步研究以修正苞叶鸭跖草属在鸭跖草科当前分类中的位置。
