Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis

Abstract

Camellia is an economically, ecologically and phylogenetically valuable genus in the family Theaceae. The frequent interspecific hybridization and polyploidization makes this genus phylogenetically and taxonomically under controversial and require detailed investigation. Chloroplast (cp) genome sequences have been used for cpDNA marker development and genetic diversity evaluation. Our research newly sequenced the chloroplast genome of Camellia japonica using Illumina HiSeq X Ten platform, and retrieved five other chloroplast genomes of Camellia previously published for comparative analyses, thereby shedding lights on a deeper understanding of the applicability of chloroplast information. The chloroplast genome sizes ranged in length from 156,607 to 157,166 bp, and their gene structure resembled those of other higher plants. There were four categories of SSRs detected in six Camellia cpDNA sequences, with the lengths ranging from 10 to 17bp. The Camellia species exhibited different evolutionary routes that lhbA and orf188, followed by orf42 and psbZ, were readily lost during evolution. Obvious codon preferences were also shown in almost all protein-coding cpDNA and amino acid sequences. Selection pressure analysis revealed the influence of different environmental pressures on different Camellia chloroplast genomes during long-term evolution. All Camellia species, except C . crapnelliana , presented the identical rate of amplification in the IR region. The datasets obtained from the chloroplast genomes are highly supportive in inferring the phylogenetic relationships of the Camellia taxa, indicating that chloroplast genome can be used for classifying interspecific relationships in this genus.

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…The most abundant were mononucleotide repeats, located in non-coding regions, and contributed to AT richness ( Figure 3). These results are consistent with most reported angiosperms [23][24][25][26][28][29][30]. The total number of SSRs was 237 in A. katsumadai, 244 in A. oxyphylla sampled from Guangdong, 247 in A. pumila, 236 in A. zerumbet, and 241 in A. oxyphylla sampled from Hainan ( Figure 3A).…”

“…The contractions and expansions at the borders of IR regions were common evolutionary events and may cause size variations of chloroplast genomes [13,[23][24][25][26][27][28][29][30]. We compared the IR-SC boundaries information of the five Alpinia chloroplast genomes ( Figure 5).…”

“…Typical chloroplast genomes of angiosperms have a generally conserved quadripartite circular structure, which consists of a large single copy (LSC) region, a small single copy (SSC) region, and two copies of inverted repeats (IRs) [16][17][18]. With the rapid development of high-throughput sequencing technologies, such as Illumina and PacBio sequencing platforms, it is now convenient to acquire complete chloroplast genome sequences [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. The chloroplast genomes have been widely utilized for species identification, the reconstruction of phylogenetic relationships, the resolution of origin problems, and the development of molecular markers [19][20][21][22][23][24][25][26][27][28][29][30].…”

The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

“…Similar to other angiosperms (Nie et al 2012;Liu et al 2013;Chi et al 2018;Yan et al 2019), the coding regions of seven Saxifragaceae chloroplast genomes are more conservative than the non-coding regions. Among the ten most divergent coding regions in this study, matK has been considered as core universal DNA barcodes in many species (Li et al 2019), and ycf1 has recently been widely applied in plant phylogeny and DNA barcoding studies (Dong et al 2015;Yang et al 2017). Besides, accD, rps19, ccsA and ndhF have also been proved to exhibit large divergence among various plant lineages and can be applied in phylogenetic studies (Ni et al 2016;Ivanova et al 2017).…”

“…In addition, comparing the complete chloroplast genome of S. sinomontana with that of other six Saxifragaceae species, we found that the size of S. sinomontana chloroplast genome is the smallest among the compared Saxifragaceae species, but the organization and gene content is highly similar. Chloroplast SSRs usually exhibit high levels of variations and are widely used in polymorphism investigations, population genetics and phylogenetic analyses (Powell et al 1995;Provan et al 1999Provan et al , 2001Flannery et al 2006;Xue et al 2012;Li et al 2019). For S. sinomontana, the number of cpSSRs (sixty-one) is moderate compared with other species of angiosperms (Liu et al 2013;Fu et al 2016;Yan et al 2019).…”