Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

Abstract

Camellia oleifera is one of the four largest woody edible oil plants in the world with high ecological and medicinal values. Due to frequent interspecific hybridization, it was difficult to study its genetics and evolutionary history. This study used C. oleifera that was collected on Hainan Island to conduct our research. The unique island environment makes the quality of tea oil higher than that of other species grown in the mainland. Moreover, a long-term geographic isolation might affect gene structure. In order to better understand the molecular biology of this species, protect excellent germplasm resources, and promote the population genetics and phylogenetic studies of Camellia plants, high-throughput sequencing technology was used to obtain the chloroplast genome sequence of Hainan C. oleifera. The results showed that the whole chloroplast genome of C. oleifera in Hainan was 156,995 bp in length, with a typical quadripartite structure of a large single copy (LSC) region of 86,648 bp, a small single copy (SSC) region of 18,297 bp, and a pair of inverted repeats (IRs) of 26,025 bp. The whole genome encoded a total of 141 genes (115 different genes), including 88 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Among these genes, nine genes contained one intron, two genes contained two introns, and four overlapping genes were also detected. The total GC content of Hainan C. oleifera’s chloroplast genome was 37.29%. The chloroplast genome structure characteristics of Hainan C. oleifera were compared with mainland C. oleifera and those of the other eight closely related Theaceae species; it was found that the contractions and expansions of the IR/LSC and IR/SSC regions affected the length of chloroplast genome. The chloroplast genome sequences of these Theaceae species were highly similar. A comparative analysis indicated that the Theaceae species were conserved in structure and evolution. A total of 51 simple sequence repeat (SSR) loci were detected in the chloroplast genome of Hainan C. oleifera, and all Camellia plants did not have pentanucleotide repeats, which could be used as a good marker in phylogenetic studies. We also detected seven long repeats, the base composition of all repeats was biased toward A/T, which was consistent with the codon bias. It was found that Hainan C. oleifera had a similar evolutionary relationship with C. crapnelliana, through the use of codons and phylogenetic analysis. This study can provide an effective genomic resource for the evolutionary history of Theaceae family.

Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

“…If the RSCU is larger than 1, it indicates that the target codon is used more frequently than expected. A value smaller than 1 indicates that the codon is used less frequently than expected 56 – 58 . Using the RSCU value as a basis of comparison, we selected one species from each of the five clades (Fig.…”

Assessment of genetic diversity in <i>Camellia oleifera</i> Abel. accessions using morphological traits and simple sequence repeat (SSR) markers

“…Camellia oleifera is a perennial economic tree species that has a long history of cultivation for more than 2,000 years. Since its characteristics of cross-pollinating, the phenotypic variations of C. oleifera germplasm were highly enriched under the environmental stress and genetic selection ( Zhang et al 2019 ). Although DNA molecular markers had been applied to study the genetic diversity of C. oleifera germplasm for a long time, it was still reliable to carry out phenotypic studies on the genetic diversity of the same species of C. oleifera with the same habitat and age.…”

The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes

“…In case of genes rps7 and rps12 that are transferred to IR of C. salebrosum plastome it is too early to conclude whether this transfer influences their substitution ratio, since the plastome sequences of only four individuals are known. In the single copy regions, the highest value was found for ycf2 gene (pi = 0.008), which is often considered as a promising barcode in many other taxa [7,35]. The second (matK) and third (rpoC2) most variable regions of Marchantiidae plastome also prove their potential as barcodes in many plant groups and are among most commonly The IR that were located genes and spacers are known from their lower substitution rates in comparison to those located in single copy parts of plastomes [6,7,13,33].…”