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The first complete chloroplast genome of Hovenia dulcis Thunb. (Rhamnaceae).

ABSTRACT: The complete chloroplast genome of Hovenia dulcis was sequenced with Illumina HiSeq 2000 platform. It was a typical quadruple structure as other plants of Hovenia with 162,962 bp in length, including a large single-copy (LSC: 90,900 bp) region and a small single-copy (SSC: 18,920 bp) which were separated by a pair of inverted repeats (IRa, b: 26,571 bp) region. The overall GC content is 36.6%. A total of 130 genes was annotated which contained 85 protein-coding genes including the Trans splicing gene of rps12, 37 tRNA genes, and 8 rRNA genes. ML phylogenetic analysis compared with 6 expressed chloroplast genomes of Rhamnaceae revealed that H. dulcis was closely related to the species of Zizyphus, and which were clustered into a group with Z. jujuba, Z. mauritiana and Z. spina-christi. Hovenia dulcis was relatively distant to other species of Berchemiella and Rhamnus, which were clustered into another group.

SUBMITTER: Liu D

PROVIDER: S-EPMC7971194 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Hovenia dulcis (Rhamnaceae).

Project description:The first complete chloroplast (cp) genome of Hovenia dulcis was reported in this study. The H. dulcis cp genome was 161,636 bp long with two inverted repeat (IR) regions of 26,574 bp, the large single-copy (LSC) region of 89,574 bp, and the small single-copy (SSC) region of 18,914 bp. The cp genome of this species contained 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 36.6%. Phylogenetic analysis based on the complete cp genomes within the Rhamnaceae family suggests that H. dulcis is closer to the genus of Ziziphus.

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Characterization of the complete chloroplast genome of Hovenia acerba (Rhamnaceae).

Project description:Hovenia acerba is a widely distributed species with economic, ornamental, and medicinal value in China. In this study, we assembled and characterized the complete chloroplast genome of H. acerba for the first time. The circular genome has a quadripartite structure with 161,651 bp in length and contains a pair of 26,619 bp inverted repeat (IR) regions, separated by the large single-copy (LSC, 89,443 bp) region and small single-copy (SSC, 18,970 bp) region. The plastid genome harbours 104 unique genes, including 72 protein-coding genes, 28 tRNAs, and four rRNAs. The overall GC content of the whole genome was 36.7%. Further, the phylogenetic analysis showed that H. acerba clustered together with Ziziphus genus. The complete chloroplast genome of H. acerba will provide important information for phylogenetic and evolutionary studies in Rhamnaceae, as well as the other closely related family.

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Project description:Hovenia acerba Lindl. is an important medicinal plant, for which complete chloroplast genome (Accession: MN782301) was sequenced, assembled and annotated. The genome size is 161,668 bp and the overall GC content is 36.69%, with large single-copy (LSC, 89,451bp) regions, small single-copy (SSC, 18,979 bp) regions, and two inverted repeat regions (IRs, 26,619 bp each). A total of 130 genes are successfully annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic relationships showed that H. acerba is closely related to the species of Ziziphus genus.

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The complete chloroplast genome of Rhamnus globosa (Rhamnaceae).

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The complete chloroplast genome sequence of Berchemia berchemiifolia (Rhamnaceae).

Project description:The complete chloroplast genome sequence of Berchemia berchemiifolia, rare plant to Korea, was determined in this study. The total genome size was 160,410?bp in length, containing a pair of inverted repeats (IRs) of 26,514?bp, which were separated by a large single copy (LSC) and small single copy (SSC) of 88,627?bp and 18,755?bp, respectively. The overall GC contents of the chloroplast genome were 37.2%. One hundred twenty nine genes were annotated, including 84 protein coding genes, 37 tRNA genes, and 8 rRNA genes. In these genes, 18 genes contained one or two introns. The phylogenetic tree showed that Berchemia berchemiifolia was most closely related to Berchemiella wilsonii.

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The complete chloroplast genome of Ziziphus jujuba cv. Bokjo (Rhamnaceae).

Project description:We have sequenced the Ziziphus jujuba cv. Bokjo chloroplast genome by de novo assembly using next-generation sequencing. The complete circular chloroplast genome consisted of 161,714 bp and contained four parts: a large single-copy (LSC) region of 89,323 bp, a small single-copy (SSC) region of 19,361 bp, and two inverted repeat regions (IRa and IRb) of 26,515 bp each. The genome annotation predicted a total of 110 genes, including 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis demonstrated the close taxonomic relationship between Z. jujuba cv. Bokjo and two other members of the Ziziphus genus, Z. spina-christi and Z. mauritiana. We found 135 polymorphic loci, 63 single nucleotide polymorphism (SNP) and 72 insertion-deletion (InDel), from the comparison of Z. jujuba cultivar Bokjo and Z. jujuba reference (NC_030299). The polymorphic loci could be used for the differentiation of Z. jujuba genetic resources and for breeding in the future.

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The complete chloroplast genome of Rhamnus crenata Siebold & Zuccarini (Rhamnaceae).

Project description:Rhamnus crenata Siebold & Zuccarini is deciduous shrub or small tree plant that widely distributed in temperate and tropical regions of East to Southeast Asia. It has a chloroplast genome structure similar to that of other species of Rhamnus. It is 160,454 bp in size, including a large single-copy (LSC) region of 88,884 bp, a small single-copy (SSC) region of 18,734 bp and a pair of inverted repeats (IRs) of 26,418 bp. A total of 122 genes were annotated, including 80 protein-coding genes, 38 transfer RNA (tRNA) genes, and 4 rRNA genes. The overall GC content is 30.71%. Phylogenetic analysis shows that R. crenata is clustered with R. taquetii and R. globosa.

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The complete chloroplast genome sequence of Rhamnella wilsonii Schneid (Rhamnaceae).

Project description:Rhamnella wilsonii Schneid 1914 is a member of the Rhamnaceae and endemic to China. In this study, the complete chloroplast genome of R. wilsonii was sequenced and assembled. The complete chloroplast genome was 160,049 bp in length, including a pair of inverted repeats (IRs) of 26,502 bp, one large single copy (LSC) region of 88,274 bp and one small single copy (SSC) region of 18,771 bp. The genome contained 129 genes, including 8 rRNA genes, 37 tRNA genes and 84 protein-coding genes. The overall GC content of the complete chloroplast genome was 37.15%. The phylogenetic analysis demonstrated that R. wilsonii is closely related to R. martinni. This study provides basic information for further studies on the identification and evolution of R. wilsonii and Rhamnella from genomic perspective.

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The complete chloroplast genome sequence of Ardisia crispa Thunb.

Project description:Ardisia crispa (Thunb.) A. DC. belongs to the genus Ardisia (Myrsinaceae). It is a traditional medicinal plant widely used to treat inflammatory-related diseases in southern China. Here, we provide the complete chloroplast genome of A. crispa from Laibin, Guangxi, PR China using Illumina high-throughput sequencing approach. The total length of the chloroplast genome is 156,709 bp, including a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats IRa and IRb regions which are separated by the LSC and SSC, with lengths of 86,301 bp, 18,411 bp, and 25,999 bp, respectively. In general, 132 genes were identified, including 93 protein-coding genes, 31 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The overall GC content is 47.82%. Phylogenetic analysis revealed that A. crispa is close to congeneric species A. mamillata.

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