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

doi:10.1016/j.pld.2021.11.009

Plant Diversity ›› 2022, Vol. 44 ›› Issue (04): 377-388.DOI: 10.1016/j.pld.2021.11.009

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

Chao Liu^a, Huan-Huan Chen^a, Li-Zhou Tang^a, Phyo Kay Khine^c, Li-Hong Han^a, Yu Song^b, Yun-Hong Tan^c,d

a College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China;
b Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, 541004, China;
c Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China;
d Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar

收稿日期:2021-05-20 修回日期:2021-11-28 出版日期:2022-07-25 发布日期:2022-08-13
通讯作者: Li-Hong Han,E-mail:hanlihong9527@126.com;Yu Song,E-mail:songyu@xtbg.ac.cn;Yun-Hong Tan,E-mail:tyh@xtbg.org.cn
基金资助:
This research was supported by the National Natural Science Foundation of China (Grant No. 32060710, 31970223, 31860005, 31860620) and Applied Basic Research Projects of Yunnan (Grant No. 2019FB057).

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

Chao Liu^a, Huan-Huan Chen^a, Li-Zhou Tang^a, Phyo Kay Khine^c, Li-Hong Han^a, Yu Song^b, Yun-Hong Tan^c,d

a College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China;
b Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, 541004, China;
c Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China;
d Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar

Received:2021-05-20 Revised:2021-11-28 Online:2022-07-25 Published:2022-08-13
Contact: Li-Hong Han,E-mail:hanlihong9527@126.com;Yu Song,E-mail:songyu@xtbg.ac.cn;Yun-Hong Tan,E-mail:tyh@xtbg.org.cn
Supported by:
This research was supported by the National Natural Science Foundation of China (Grant No. 32060710, 31970223, 31860005, 31860620) and Applied Basic Research Projects of Yunnan (Grant No. 2019FB057).

摘要/Abstract

摘要： Litsea, 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 Litsea and Laurus, Lindera, Parasassafras and Sinosassafras of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced Litsea 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 Litsea taxa. One is composed of 16 Litsea taxa and two Lindera 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 (Litsea auriculata) and 154,117 bp (Litsea pierrei). Seven of the 16 Litsea plastomes have a pair of insertions in the IRa (trnL-trnH) and IRb (ycf2) regions. The 18 plastomes of Litsea and Lindera 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 (accD, ndhJ, rbcL, rpoC2, ycf1 and ycf2) under positive selection in Litsea; these genes may play important roles in adaptation of Litsea species to various environments.

关键词: Litsea, Phylogenetic analysis, Divergent hotspots, Gene evolution

Abstract: Litsea, 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 Litsea and Laurus, Lindera, Parasassafras and Sinosassafras of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced Litsea 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 Litsea taxa. One is composed of 16 Litsea taxa and two Lindera 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 (Litsea auriculata) and 154,117 bp (Litsea pierrei). Seven of the 16 Litsea plastomes have a pair of insertions in the IRa (trnL-trnH) and IRb (ycf2) regions. The 18 plastomes of Litsea and Lindera 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 (accD, ndhJ, rbcL, rpoC2, ycf1 and ycf2) under positive selection in Litsea; these genes may play important roles in adaptation of Litsea species to various environments.

Key words: Litsea, Phylogenetic analysis, Divergent hotspots, Gene evolution

Chao Liu, Huan-Huan Chen, Li-Zhou Tang, Phyo Kay Khine, Li-Hong Han, Yu Song, Yun-Hong Tan. Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae)[J]. Plant Diversity, 2022, 44(04): 377-388.

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

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

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