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樟科月桂亚族(樟科月桂族)一个单系类群的质体基因组进化

Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae).

作者信息

Liu Chao, Chen Huan-Huan, Tang Li-Zhou, Khine Phyo Kay, Han Li-Hong, Song Yu, Tan Yun-Hong

机构信息

College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China.

Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.

出版信息

Plant Divers. 2021 Dec 14;44(4):377-388. doi: 10.1016/j.pld.2021.11.009. eCollection 2022 Jul.

DOI:10.1016/j.pld.2021.11.009
PMID:35967258
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9363652/
Abstract

, a non-monophyletic group of the tribe Laureae (Lauraceae), plays important roles in the tropical and subtropical forests of Asia, Australia, Central and North America, and the islands of the Pacific. However, intergeneric relationships between and , , and of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced plastomes, together with 47 Laureae plastomes obtained from public databases, representing six genera of the Laureae. Our results highlight two highly supported monophyletic groups of taxa. One is composed of 16 taxa and two taxa. The 18 plastomes of these taxa were further compared for their gene structure, codon usage, contraction and expansion of inverted repeats, sequence repeats, divergence hotspots, and gene evolution. The complete plastome size of newly sequenced taxa varied between 152,377 bp () and 154,117 bp (). Seven of the 16 plastomes have a pair of insertions in the IRa (-) and IRb () regions. The 18 plastomes of and taxa exhibit similar gene features, codon usage, oligonucleotide repeats, and inverted repeat dynamics. The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots, which are located in the same regions. We also identified six protein coding genes (, , , , and ) under positive selection in ; these genes may play important roles in adaptation of species to various environments.

摘要

(某属)是樟科月桂族的一个非单系类群,在亚洲、澳大利亚、中北美洲以及太平洋诸岛的热带和亚热带森林中发挥着重要作用。然而,月桂族中该属与其他属(如[其他属名1]、[其他属名2]、[其他属名3]和[其他属名4])之间的属间关系仍未解决。在本研究中,我们对七个新测序的该属质体基因组进行了系统发育分析,并结合从公共数据库中获取的47个月桂族质体基因组,这些质体基因组代表了月桂族的六个属。我们的结果突出了两个得到高度支持的该属分类群单系类群。一个类群由16个该属分类单元和两个其他属分类单元组成。进一步比较了这些分类单元的18个质体基因组的基因结构、密码子使用、反向重复序列的收缩和扩展、序列重复、分歧热点以及基因进化。新测序分类单元的完整质体基因组大小在152,377 bp([具体物种1])和154,117 bp([具体物种2])之间变化。16个该属质体基因组中的7个在IRa(-[具体位置1])和IRb(-[具体位置2])区域有一对插入。该属和其他属分类单元的18个质体基因组表现出相似的基因特征、密码子使用、寡核苷酸重复和反向重复动态。这些分类单元中出现频率最高的密码子倾向于以A/T结尾,并且每个质体基因组都有九个分歧热点,它们位于相同区域。我们还在该属中鉴定出六个受到正选择的蛋白质编码基因([基因名1]、[基因名2]、[基因名3]、[基因名4]、[基因名5]和[基因名6]);这些基因可能在该属物种适应各种环境中发挥重要作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/044cd785c45e/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/51579fca792b/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/a7028143767e/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/79683e363cad/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/02ecd9868779/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/691d4281ce17/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/1af70705d6c3/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/044cd785c45e/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/51579fca792b/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/a7028143767e/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/79683e363cad/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/02ecd9868779/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/691d4281ce17/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/1af70705d6c3/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce0a/9363652/044cd785c45e/gr7.jpg

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