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Genes 2017, 8(12), 340; doi:10.3390/genes8120340

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

1,†,* , 2,†
and
1,*
1
Forest Key Laboratory of Shaanxi Province, College of Forestry, Northwest A & F University, Yangling 712100, China
2
Shaanxi Province Key Laboratory of Jujube, College of Life Science, Yan’an University, Yan’an 716000, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 10 August 2017 / Revised: 14 November 2017 / Accepted: 23 November 2017 / Published: 24 November 2017
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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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. View Full-Text
Keywords: Ziziphus; chloroplast genome; phylogenetic analysis; microsatellite markers; Ziziphus spina-christi Ziziphus; chloroplast genome; phylogenetic analysis; microsatellite markers; Ziziphus spina-christi
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Huang, J.; Chen, R.; Li, X. Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species. Genes 2017, 8, 340.

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