Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species

Abstract

Ziziphus Mill. (Rhamnaceae) is comprised of about 170 species that are mainly distributed in tropical to subtropical regions, with few in the temperate zone. Several Ziziphus fruit tree species are important energy, nutrient, and medicinal resources for human populations, particularly for those living in rural regions. To date, limited genomic information is available for this genus. Here, we assembled the complete chloroplast genomes of four best known Ziziphus species, i.e., Ziziphus jujuba, Ziziphus acidojujuba, Ziziphus mauritiana, and Ziziphus spina-christi, based on the Illumina Paired-end sequencing method. The chloroplast genomes of the four Ziziphus species are all very similar to one another, and exhibit structural, gene content, and order characteristics that are similar to other flowering plants. The entire chloroplast genome encodes 113 predicted unique genes (85 protein-coding genes, 8 rRNA, and 37 tRNA), 17 of which are duplicated in the inverted repeat regions. Rich single sequence repeats loci (217) were detected in Z. jujuba and 106 SSR loci, composed of A/T, displayed polymorphism across the four species by comparative genomic analysis. We found only four genes under positive selection between Z. jujuba and Z. acidojujuba, and two genes for Z. mauritiana vs. Z. spina-christi, respectively, while half of the 78 protein-coding genes experienced positive selection between the two groups. Phylogenetic analyses revealed that Ziziphus (Rhamnaceae) was sister to Elaeagnaceae, and the four species of Ziziphus were clustered into two groups (Z. jujuba and Z. acidojujuba, Z. mauritiana and Z. spina-christi). Our results provide genomic resources for intrageneric classifications of Ziziphus, and valuable genetic markers for investigating the population genetics and biogeography of closely related Ziziphus species.

Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution

“…Chloroplast repeats are potentially useful genetic resources to investigate population genetics and biogeography of allied taxa [ 26 ]. Analyses of various cp genomes revealed that repeat sequences are essential to induce indels and substitutions [ 27 ].…”

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

“…Repetitive sequences in plastid genomes play an essential role in population genetics and biogeography studies [51,52], and these repeats may result from slipped-strand mispairing and improper recombination [53]. In this study, short dispersed repeats (SDRs) analysis found 22 forward, 0 reverse, 0 complement and 20 palindromic repeats in the plastid genome of B. chinense ( Figure 4A), of which 32 were 30-40 bp in length, 7 were 41-50 bp in length, and 3 exceeded 70 bp in length ( Figure 4B).…”

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

“…Due to its abundant polymorphism, high stability, codominant inheritance and ease of use, SSRs have gradually been a popular and robust tool for population genetic analysis in non-model organisms [43]. It is believed that the threshold for SSRs screening should be over 8 bp, as SSRs of 8 bp or longer tend towards slip-strand mispairing (SSM), which is considered the main mutational mechanism that has some influence on SSRs [7,16]. In the present study, we set parameters over 8 bp to identify the potential SSRs in the chloroplast genome of broomcorn millet, together with other five related species.…”

“…The phylogenomic analysis of cp genomes is of great value in providing resolution and support for evolutionary relationships of angiosperms. Furthermore, it will shed light on the cp genome evolution, such as sequence inversion [9,14], gene loss and gain [15,16], and structure variation [17,18].…”