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

Moonkyo Kim; Jin Hee Park; Jinsu Gil; Jung Sung Kim; Hyoung Tae Kim; Ha Kyung Oh; Kyeong Hee Lee; Minjee Lee; Jungho Lee; Yi Lee

doi:10.1080/23802359.2022.2131366

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

Moonkyo Kim, Jin Hee Park, Jinsu Gil, Jung Sung Kim, Hyoung Tae Kim, Ha Kyung Oh, Kyeong Hee Lee, Minjee Lee, Jungho Lee, Yi Lee

Department of Crop Science

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	1805-1806
Number of pages	2
Journal	Mitochondrial DNA Part B: Resources
Volume	7
Issue number	10
DOIs	https://doi.org/10.1080/23802359.2022.2131366
State	Published - 2022

Keywords

Chloroplast genome
next-generation sequencing
Ziziphus jujuba

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10.1080/23802359.2022.2131366

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title = "The complete chloroplast genome of Ziziphus jujuba cv. Bokjo (Rhamnaceae)",

abstract = "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.",

keywords = "Chloroplast genome, next-generation sequencing, Ziziphus jujuba",

author = "Moonkyo Kim and Park, {Jin Hee} and Jinsu Gil and Kim, {Jung Sung} and Kim, {Hyoung Tae} and Oh, {Ha Kyung} and Lee, {Kyeong Hee} and Minjee Lee and Jungho Lee and Yi Lee",

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year = "2022",

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T1 - The complete chloroplast genome of Ziziphus jujuba cv. Bokjo (Rhamnaceae)

AU - Kim, Moonkyo

AU - Park, Jin Hee

AU - Gil, Jinsu

AU - Kim, Jung Sung

AU - Kim, Hyoung Tae

AU - Oh, Ha Kyung

AU - Lee, Kyeong Hee

AU - Lee, Minjee

AU - Lee, Jungho

AU - Lee, Yi

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Chloroplast genome

KW - next-generation sequencing

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

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Keywords

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