The first complete plastome sequence from the family Cardiopteridaceae, Gonocaryum lobbianum (Miers) Kurz

Sangjin Jo, Young Kee Kim, Se Hwan Cheon, Ki-Joong Kim

Research output: Contribution to journalArticle

Abstract

In this study, we determined the complete plastome sequence of Gonocaryum lobbianum (Miers) Kurz (Cardiopteridaceae) (NCBI acc. no. MK390345). This is the first reported complete plastome sequence from the family Cardiopteridaceae of the order Aquifoliales. The complete plastome of G. lobbianum is 158,905 bp in length and consists of a large single copy of 87,705 bp and a small single copy of 19,346 bp, separated by two inverted repeats of 25,927 bp. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. The rpoA gene was pseudogenized because of deletion and following frame-shift mutations. We also confirmed the pseudonization of rpoA gene using PCR and conventional Sanger sequencing methods. Sixteen genes contain one intron and two genes have two introns. The average A-T content of the plastome is 62.7%. A total of 73 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that G. lobbianum is a sister group of Aquifoliaceae-Helwingiaceae with 100% bootstrap value. The Aquifoliales clade is a sister group to the Apiales-Asterales-Dipsacales clade with 100% bootstrap support.

Original languageEnglish
Pages (from-to)1025-1026
Number of pages2
JournalMitochondrial DNA Part B: Resources
Volume4
Issue number1
DOIs
Publication statusPublished - 2019 Jan 2

Fingerprint

Genes
Aquifoliaceae
Introns
Frameshift Mutation
Transfer RNA
rRNA Genes
Microsatellite Repeats
Genome
Polymerase Chain Reaction
Proteins

Keywords

  • Aquifoliales
  • Cardiopteridaceae
  • Gonocaryum lobbianum
  • Platome
  • rpoA pseudogene

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

The first complete plastome sequence from the family Cardiopteridaceae, Gonocaryum lobbianum (Miers) Kurz. / Jo, Sangjin; Kim, Young Kee; Cheon, Se Hwan; Kim, Ki-Joong.

In: Mitochondrial DNA Part B: Resources, Vol. 4, No. 1, 02.01.2019, p. 1025-1026.

Research output: Contribution to journalArticle

@article{77e4cf5434e04309855efd4d13369463,
title = "The first complete plastome sequence from the family Cardiopteridaceae, Gonocaryum lobbianum (Miers) Kurz",
abstract = "In this study, we determined the complete plastome sequence of Gonocaryum lobbianum (Miers) Kurz (Cardiopteridaceae) (NCBI acc. no. MK390345). This is the first reported complete plastome sequence from the family Cardiopteridaceae of the order Aquifoliales. The complete plastome of G. lobbianum is 158,905 bp in length and consists of a large single copy of 87,705 bp and a small single copy of 19,346 bp, separated by two inverted repeats of 25,927 bp. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. The rpoA gene was pseudogenized because of deletion and following frame-shift mutations. We also confirmed the pseudonization of rpoA gene using PCR and conventional Sanger sequencing methods. Sixteen genes contain one intron and two genes have two introns. The average A-T content of the plastome is 62.7{\%}. A total of 73 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that G. lobbianum is a sister group of Aquifoliaceae-Helwingiaceae with 100{\%} bootstrap value. The Aquifoliales clade is a sister group to the Apiales-Asterales-Dipsacales clade with 100{\%} bootstrap support.",
keywords = "Aquifoliales, Cardiopteridaceae, Gonocaryum lobbianum, Platome, rpoA pseudogene",
author = "Sangjin Jo and Kim, {Young Kee} and Cheon, {Se Hwan} and Ki-Joong Kim",
year = "2019",
month = "1",
day = "2",
doi = "10.1080/23802359.2019.1584064",
language = "English",
volume = "4",
pages = "1025--1026",
journal = "Mitochondrial DNA Part B: Resources",
issn = "2380-2359",
publisher = "Taylor and Francis Ltd.",
number = "1",

}

TY - JOUR

T1 - The first complete plastome sequence from the family Cardiopteridaceae, Gonocaryum lobbianum (Miers) Kurz

AU - Jo, Sangjin

AU - Kim, Young Kee

AU - Cheon, Se Hwan

AU - Kim, Ki-Joong

PY - 2019/1/2

Y1 - 2019/1/2

N2 - In this study, we determined the complete plastome sequence of Gonocaryum lobbianum (Miers) Kurz (Cardiopteridaceae) (NCBI acc. no. MK390345). This is the first reported complete plastome sequence from the family Cardiopteridaceae of the order Aquifoliales. The complete plastome of G. lobbianum is 158,905 bp in length and consists of a large single copy of 87,705 bp and a small single copy of 19,346 bp, separated by two inverted repeats of 25,927 bp. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. The rpoA gene was pseudogenized because of deletion and following frame-shift mutations. We also confirmed the pseudonization of rpoA gene using PCR and conventional Sanger sequencing methods. Sixteen genes contain one intron and two genes have two introns. The average A-T content of the plastome is 62.7%. A total of 73 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that G. lobbianum is a sister group of Aquifoliaceae-Helwingiaceae with 100% bootstrap value. The Aquifoliales clade is a sister group to the Apiales-Asterales-Dipsacales clade with 100% bootstrap support.

AB - In this study, we determined the complete plastome sequence of Gonocaryum lobbianum (Miers) Kurz (Cardiopteridaceae) (NCBI acc. no. MK390345). This is the first reported complete plastome sequence from the family Cardiopteridaceae of the order Aquifoliales. The complete plastome of G. lobbianum is 158,905 bp in length and consists of a large single copy of 87,705 bp and a small single copy of 19,346 bp, separated by two inverted repeats of 25,927 bp. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. The rpoA gene was pseudogenized because of deletion and following frame-shift mutations. We also confirmed the pseudonization of rpoA gene using PCR and conventional Sanger sequencing methods. Sixteen genes contain one intron and two genes have two introns. The average A-T content of the plastome is 62.7%. A total of 73 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that G. lobbianum is a sister group of Aquifoliaceae-Helwingiaceae with 100% bootstrap value. The Aquifoliales clade is a sister group to the Apiales-Asterales-Dipsacales clade with 100% bootstrap support.

KW - Aquifoliales

KW - Cardiopteridaceae

KW - Gonocaryum lobbianum

KW - Platome

KW - rpoA pseudogene

UR - http://www.scopus.com/inward/record.url?scp=85062454823&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85062454823&partnerID=8YFLogxK

U2 - 10.1080/23802359.2019.1584064

DO - 10.1080/23802359.2019.1584064

M3 - Article

AN - SCOPUS:85062454823

VL - 4

SP - 1025

EP - 1026

JO - Mitochondrial DNA Part B: Resources

JF - Mitochondrial DNA Part B: Resources

SN - 2380-2359

IS - 1

ER -