Open AccessCharacterization of 20 complete plastomes from the tribe Laureae (Lauraceae) and distribution of small inversions
Author(s) -
Sangjin Jo,
Sang Hyun Kim,
Se Hwan Cheon,
Qingxia Fan,
Ki Joong Kim
Publication year - 2019
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0224622
Subject(s) - ndhf , chloroplast dna , biology , intergenic region , botany , evolutionary biology , phylogenetic tree , genetics , genome , gene
Lindera Thunb. (Lauraceae) consists of approximately 100 species, mainly distributed in the temperate and tropical regions of East Asia. In this study, we report 20 new, complete plastome sequences including 17 Lindera species and three related species, Actinodaphne lancifolia , Litsea japonica and Sassafras tzumu . The complete plastomes of Lindera range from 152,502 bp ( L . neesiana ) to 154,314 bp ( L . erythrocarpa ) in length. Eleven small inversion (SI) sites are documented among the plastomes. Six of the 11 SI sites are newly reported and they locate in rpo B- trn C, psb C- trn S, pet A- psb J, rpo A and ycf 2 regions. The distribution patterns of SIs are useful for species identification. An average of 83 simple sequence repeats (SSRs) were detected in each plastome. The mono-SSRs accounted for 72.7% of total SSRs, followed by di- (12.4%), tetra- (9.4%), tri- (4.2%), and penta-SSRs (1.3%). Of these SSRs, 64.6% were distributed in an intergenic spacer (IGS) region. In addition, 79.8% of the SSRs are located in a large single copy (LSC) region. In contrast, almost no SSRs are distributed in inverted repeat (IR) regions. The SSR loci are useful to identifying species but the phylogenetic value is low because the majority of them show autapomorphic status or highly homoplastic characteristics. The nucleotide diversity (Pi) values also indicated the conserved nature of the IR region compared to LSC and small single copy (SSC) regions. Five spacer regions with high Pi values, trn H- psb A, pet A- psb J and ndh F- rpl 32, rpl 32- trn L and Ψ ycf 1- ndh F, have a potential use for the molecular identification study of Lindera and related species. Lindera species form a paraphyletic group in the plastome tree because of the inclusion of related genera such as Actinodaphne , Laurus , Litsea and Neolitsea . A former member of tribe Laureae, Sassafras , forms a clade with the tribe Cinnamomeae. The SIs do not affect the phylogenetic relationship of Laureae. This result indicated that ancient plastome captures may have contribute to the mixed intergeneric relationship of Laureae. Alternatively, the result may indicate that the morphological characters defined the genera of Lauraceae originated for several times.