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

Jian Huang,Ruihong Chen,Xingang Li

doi:10.3390/genes8120340

Jian Huang, Ruihong Chen + Show 1 more

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https://doi.org/10.3390/genes8120340

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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.

Highlights

Ziziphus (Mill.: Rhamnaceae) is comprised of about 170 species widely distributed in tropical and subtropical regions, including a few in the temperate zone [1,2]
By screening these paired-end reads through alignment with reference chloroplast genomes, 12,672,000 reads were mapped to the reference genome
Four junction regions between inverted repeat (IR) and SSC/LSC and intragenic regions were confirmed by PCR amplification and Sanger sequencing

Summary

Introduction

Ziziphus (Mill.: Rhamnaceae) is comprised of about 170 species widely distributed in tropical and subtropical regions, including a few in the temperate zone [1,2]. A few species of Ziziphus, those growing in Asia, Africa, and South America, produce edible and multi-nutritional fruits, supplementing human diets and to farmers income [1]. Chinese jujube (Ziziphus jujuba) has become the most widely planted Ziziphus fruit tree in the temperate zone. Z. jujuba and its progenitor, Ziziphus acidojujuba, native to the North China, were introduced to central Asia and Europe, including Iran, Israel, and Romania through the “Silk Road” trade thousands of years ago, and more recently to North America [2,3]. Known as India jujube, is native to a wide tropical region from Vietnam, India to Sahel, and domesticated in India.

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