Characteristics of chloroplast genome and phylogenetic analysis of Diospyros sutchuensis with extremely small populations

Abstract

Diospyros sutchuensis is a national protected wild plant species with narrow distribution and extremely small population in southwestern China. At present, the genomic information of this species is lacking and its phylogenetic relationships among Diospyros remain unclear. In this study, the chloroplast genome of D. sutchuensis was sequenced by Illumina platform, assembled and annotated by Getorganelle v1.7.3.4 and PGA, and analyzed by DnaSP 6.12.03 for sequence comparison, REPuter, Tandem Reapeats Finder, MISA for repetitive sequences, CodonW1.4 for codon usage bias, and EasyCodemL for selection pressure. Meanwhile, based on four different chloroplast genome sequence datasets, the phylogenetic relationships between D. sutchuensis and 11 Diospyros species were analyzed using IQtree. The results were as follows: (1) The chloroplast genome of D. sutchuensis was 157 917 bp in length, including two inverted repeats (IRs) of 26 111 bp, which was separated by large single copy (LSC) and short single copy (SSC) of 87 303 bp and 18 392 bp, respectively. The GC content was 37.4%. (2) The genome contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A total of 49 long repeats, 27 tandem repeats, and 34 simple sequence repeats were identified. There were 31 high-frequency codons in protein-coding genes, most of them ended in A or U, and the most used codons were the ones encoding leucine. The coding regions were more conserved than the non-coding ones, and 10 regions were identified as most divergent hotspots for potential molecular markers. There had been positive selection on ndhB, ndhG, ndhI, rbcL, rpoB, petB, petD and rps12 among protein-coding genes. (3) Phylogenetic analyses showed that D. sutchuensis was closely related to D. rhombifolia and D. cathayensis. Together with D. hainanensis, these four species formed a monophyletic group. The phylogenetic tree constructed from the chloroplast genomes had the highest support values, indicating that the chloroplast genomes with most variable and informative sites are more suitable for phylogenetic studies of Diospyros. The results provide useful chloroplast genomic resources for germplasm identification, genetic diversity conservation, repopulation, and phylogenetic analysis of D. sutchuensis as well as Diospyros.

Keywords

• diospyros sutchuensis
• chloroplast genome
• repeat sequence
• selection pressure
• phylogenetic analysis