Comparative plastome analysis of Arundinelleae (Poaceae, Panicoideae), with implications for phylogenetic relationships and plastome evolution.

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Li-Qiong Jiang, Bryan T Drew, Watchara Arthan, Guo-Ying Yu, Hong Wu, Yue Zhao, Hua Peng, Chun-Lei Xiang
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引用次数: 0

Abstract

Background: Arundinelleae is a small tribe within the Poaceae (grass family) possessing a widespread distribution that includes Asia, the Americas, and Africa. Several species of Arundinelleae are used as natural forage, feed, and raw materials for paper. The tribe is taxonomically cumbersome due to a paucity of clear diagnostic morphological characters. There has been scant genetic and genomic research conducted for this group, and as a result the phylogenetic relationships and species boundaries within Arundinelleae are poorly understood.

Results: We compared and analyzed 11 plastomes of Arundinelleae, of which seven plastomes were newly sequenced. The plastomes range from 139,629 base pairs (bp) (Garnotia tenella) to 140,943 bp (Arundinella barbinodis), with a standard four-part structure. The average GC content was 38.39%, but varied in different regions of the plastome. In all, 110 genes were annotated, comprising 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Furthermore, 539 simple sequence repeats, 519 long repeats, and 10 hyper-variable regions were identified from the 11 plastomes of Arundinelleae. A phylogenetic reconstruction of Panicoideae based on 98 plastomes demonstrated the monophyly of Arundinella and Garnotia, but the circumscription of Arundinelleae remains unresolved.

Conclusion: Complete chloroplast genome sequences can improve phylogenetic resolution relative to single marker approaches, particularly within taxonomically challenging groups. All phylogenetic analyses strongly support the monophyly of Arundinella and Garnotia, respectively, but the monophylly of Arundinelleae was not well supported. The intergeneric phylogenetic relationships within Arundinelleae require clarification, indicating that more data is necessary to resolve generic boundaries and evaluate the monophyly of Arundinelleae. A comprehensive taxonomic revision for the tribe is necessary. In addition, the identified hyper-variable regions could function as molecular markers for clarifying phylogenetic relationships and potentially as barcoding markers for species identification in the future.

Arundinelleae (Poaceae, Panicoideae) 的比较质体分析,及其对系统发育关系和质体进化的影响。
背景:Arundinelleae 是禾本科(Poaceae)中的一个小族,分布广泛,包括亚洲、美洲和非洲。Arundinelleae 的若干种被用作天然饲料、饲料和造纸原料。由于缺乏明确的形态学诊断特征,该族在分类学上非常繁琐。对该类群的遗传和基因组研究很少,因此对 Arundinelleae 内的系统发育关系和物种界限知之甚少:结果:我们比较并分析了 Arundinelleae 的 11 个质粒,其中 7 个质粒是新测序的。这些质粒的碱基对从 139,629 碱基对(Garnotia tenella)到 140,943 碱基对(Arundinella barbinodis)不等,具有标准的四部分结构。平均 GC 含量为 38.39%,但在质体的不同区域有所不同。共注释了 110 个基因,包括 76 个蛋白质编码基因、30 个 tRNA 基因和 4 个 rRNA 基因。此外,还从 Arundinelleae 的 11 个质体中发现了 539 个简单序列重复序列、519 个长重复序列和 10 个超变区。基于 98 个质粒的 Panicoideae 系统进化重建表明 Arundinelleae 和 Garnotia 为单系,但 Arundinelleae 的周系仍未确定:结论:与单一标记方法相比,完整的叶绿体基因组序列可提高系统发育的分辨率,尤其是在具有分类学挑战性的类群中。所有系统发育分析都分别强烈支持 Arundinella 和 Garnotia 的单系性,但 Arundinelleae 的单系性没有得到很好的支持。Arundinelleae内的属间系统发育关系需要澄清,这表明需要更多的数据来确定属的界限和评估Arundinelleae的单系性。有必要对该族进行全面的分类学修订。此外,已确定的超变异区可作为分子标记,用于澄清系统发生关系,并有可能作为条形码标记用于未来的物种鉴定。
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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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