Blumea属(Astoroideae,菊科)约100种,包括草药,灌木,和小树。由于分子标记的多态性较低,以前的研究无法解决Blumea属的分类学问题和系统发育。因此,需要确定合适的多态性区域。这里,我们从头组装了三种Blumea物种B.oxyodonta的质体,B.tenella,和balsamifica,并将其与其他26种Astoroideae进行比较。这些物种有四分体,基因含量相似,基因组组织,包括113个基因的反向重复收缩和扩展,包括80个蛋白质编码,29转移RNA,和4个核糖体RNA基因。密码子使用的比较分析,氨基酸频率,微卫星重复,寡核苷酸重复,过渡和变性置换揭示了新组装的Blumea物种之间的高度相似性。我们确定了10个核苷酸多样性高于0.02的高度多态性区域,包括rps16-trnQ,ycf1,ndhF-rpl32,petN-psbM,和rpl32-trnL,它们可能适合于健壮的发展,正宗,和具有成本效益的标记,用于条形码和推断Blumea属的系统发育。在这些高度多态的区域中,五个区域也与寡核苷酸重复序列共同发生,并支持使用重复序列作为鉴定多态性位点的代理。系统发育分析揭示了Inuleae部落中Blumea和Pluchea之间的密切关系。在部落层面,我们的系统发育支持了根植为Gnapalieae的Astereae和Anthemideae之间的姐妹关系,Calenduleae,和Senecioneae。这些结果与最近的研究相矛盾,这些研究报告了“Senecioneae和Anthemideae”与“Aereae和Gnapalieae”之间的姐妹关系,或根植为Calenduleae的Aereae和Gnapalieae之间的姐妹关系,Anthemideae,然后使用核基因组序列。在质体和核基因组数据之间的部落水平上观察到的相互矛盾的系统发育信号需要进一步研究。
The genus
Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus
Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three
Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for barcoding and inference of the phylogeny of the genus
Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between
Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between \"Senecioneae and Anthemideae\" and \"Astereae and Gnaphalieae\" or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.