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Chloroplast Genome Characteristics and Phylogeny of the Genus Lycoris (Amaryllidaceae)
FU Wen-fo, XIAO Tao, ZHANG Yong-hong
Subtropical Plant Science
2023, 52 (4):
271-286.
DOI: 10.3969/j.issn.1009-7791.2023.04.001
In this study, the basic characteristics and phylogenetic relationship of chloroplast genome sequences from 17 species of Lycoris were analyzed. The results showed that the chloroplast genomes of Lycoris had a typical quadripartite circle structure with a total length of 158 335–158 761 bp and a total GC content of 37.7%–37.8%. The number of genes was 133–137, and the number of protein-coding genes, rRNA genes, and tRNA genes were identical in different species. There were 41–57 interspersed repeats and 66–74 SSR loci detected, among which single nucleotide A/T repeats were the most frequent. Codon preference analysis showed that the number of coding codons ranged from 26 448 to 26 740. The RSCU values of 31 codons were greater than 1 and the third base of 29 codons were A or U, which indicated that Lycoris plant preferred codons ended with A or U. The results of chloroplast genome alignment and collinearity analysis exhibited highly conservative with no rearrangement and inversion observed. Higher variation frequency of non-coding regions versus coding regions was detected. The IR boundary analysis showed that rpl22, rps19 and ndhF genes in some species crossed the JLB or JSB boundary due to the contraction and expansion of the IR region. Nucleotide polymorphism analysis detected 7 highly variable genes or intergenic regions, trnG-UCC, atpF-atpH, psbC-trnS-UGA-psbZ, trnG-GCC-psbZ, rpl32, trnL-UAG- rpl32-ccsA, rps15-ycf1, which could be used as molecular markers for phylogenetic analysis. The molecular phylogenetic tree showed that all Lycoris species clustered closely and formed a monophyly, which supported the independent taxonomic status of the genus. Two traditional subgenera, Symmanthus and Lycoris, didn’t form monophyly separately, although distinguished in stamen and corolla. And it was still doubtable on the intrageneric circumscription based on the relative position of stamens and perianth. In addition, the phylogenetic analysis supported the perspective of the hybrid origin of L. anhuiensis, L. houdyshelii, L. straminea and L. rosea, with potential maternal species recommended.
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