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

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 livi...

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Autores principales: Huang, Jian, Chen, Ruihong, Li, Xingang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748658/
https://www.ncbi.nlm.nih.gov/pubmed/29186778
http://dx.doi.org/10.3390/genes8120340
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author Huang, Jian
Chen, Ruihong
Li, Xingang
author_facet Huang, Jian
Chen, Ruihong
Li, Xingang
author_sort Huang, Jian
collection PubMed
description 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.
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spelling pubmed-57486582018-01-07 Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species Huang, Jian Chen, Ruihong Li, Xingang Genes (Basel) Article 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. MDPI 2017-11-24 /pmc/articles/PMC5748658/ /pubmed/29186778 http://dx.doi.org/10.3390/genes8120340 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Huang, Jian
Chen, Ruihong
Li, Xingang
Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species
title Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species
title_full Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species
title_fullStr Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species
title_full_unstemmed Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species
title_short Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species
title_sort comparative analysis of the complete chloroplast genome of four known ziziphus species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748658/
https://www.ncbi.nlm.nih.gov/pubmed/29186778
http://dx.doi.org/10.3390/genes8120340
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