Literature DB >> 33553639

Chloroplast genome organization and phylogeny of Gynochthodes cochinchinensis (DC.) Razafim. & B. Bremer (Rubiaceae).

Mary Ann C Bautista1,2,3, Wenqin Tao4, Yan Zheng2, Yunfei Deng2,3, Tao Chen1,3, Shenyu Miao4.   

Abstract

Gynochthodes cochinchinensis previously known as Morinda cochinchinensis is considered as potential medicinal plant in family Rubiaceae. In this paper, the complete chloroplast genome of G. cochinchinensis was sequenced and characterized for the first time. The cp genome of G. cochinchinensis was 153,022 bp in length containing a large single copy region (83,799 bp), a small single copy region (17,591 bp), and a pair of inverted repeat regions (25,816 bp). It has a total of 131 genes, comprising of 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Phylogenetic analysis revealed that Gynochthodes cochinchinensis together with Gynochthodes officinalis were closely related to genus Morinda.
© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

Entities:  

Keywords:  Gynocthodes cochinchinensis; Rubiaceae; complete chloroplast genome; phylogeny

Year:  2021        PMID: 33553639      PMCID: PMC7850335          DOI: 10.1080/23802359.2020.1862716

Source DB:  PubMed          Journal:  Mitochondrial DNA B Resour        ISSN: 2380-2359            Impact factor:   0.658


  7 in total

1.  NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.

Authors:  Ravi K Patel; Mukesh Jain
Journal:  PLoS One       Date:  2012-02-01       Impact factor: 3.240

2.  Assembling short reads from jumping libraries with large insert sizes.

Authors:  Irina Vasilinetc; Andrey D Prjibelski; Alexey Gurevich; Anton Korobeynikov; Pavel A Pevzner
Journal:  Bioinformatics       Date:  2015-06-03       Impact factor: 6.937

3.  tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.

Authors:  Patricia P Chan; Todd M Lowe
Journal:  Methods Mol Biol       Date:  2019

4.  Molecular phylogenetics and generic assessment in the tribe Morindeae (Rubiaceae-Rubioideae): how to circumscribe Morinda L. to be monophyletic?

Authors:  Sylvain G Razafimandimbison; Timothy D McDowell; David A Halford; Birgitta Bremer
Journal:  Mol Phylogenet Evol       Date:  2009-04-24       Impact factor: 4.286

5.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.

Authors:  Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2014-01-21       Impact factor: 6.937

6.  CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

Authors:  Chang Liu; Linchun Shi; Yingjie Zhu; Haimei Chen; Jianhui Zhang; Xiaohan Lin; Xiaojun Guan
Journal:  BMC Genomics       Date:  2012-12-20       Impact factor: 3.969

7.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes.

Authors:  Karin Lagesen; Peter Hallin; Einar Andreas Rødland; Hans-Henrik Staerfeldt; Torbjørn Rognes; David W Ussery
Journal:  Nucleic Acids Res       Date:  2007-04-22       Impact factor: 16.971

  7 in total
  2 in total

1.  Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species.

Authors:  Jing-Lu Feng; Li-Wei Wu; Qing Wang; Yun-Jia Pan; Bao-Li Li; Yu-Lin Lin; Hui Yao
Journal:  Biomed Res Int       Date:  2022-07-27       Impact factor: 3.246

2.  Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus.

Authors:  Eun-Kyeong Han; Won-Bum Cho; Ichiro Tamaki; In-Su Choi; Jung-Hyun Lee
Journal:  Int J Mol Sci       Date:  2021-07-05       Impact factor: 5.923

  2 in total

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