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Open AccessArticle

The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae

1
College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China
2
State Key Laboratory of Exploration and Utilization of Crop Gene Resources in 10 Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in 11 Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan 12 Agricultural University, Chengdu 600031, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Plants 2020, 9(4), 478; https://doi.org/10.3390/plants9040478
Received: 3 March 2020 / Revised: 3 April 2020 / Accepted: 4 April 2020 / Published: 9 April 2020
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species. View Full-Text
Keywords: chloroplast genome; Trifolium; divergence time; IR lacking; rearrangement; repetitive events chloroplast genome; Trifolium; divergence time; IR lacking; rearrangement; repetitive events
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Xiong, Y.; Xiong, Y.; He, J.; Yu, Q.; Zhao, J.; Lei, X.; Dong, Z.; Yang, J.; Peng, Y.; Zhang, X.; Ma, X. The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae. Plants 2020, 9, 478.

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