Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species

C Guyeux, JC Charr, HTM Tran, A Furtado, RJ Henry… - PLoS …, 2019 - journals.plos.org
Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of
conservation in plants. Whole chloroplast genomes can now be readily obtained for plant …

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

J Cheng, X Zeng, G Ren, Z Liu - BMC bioinformatics, 2013 - Springer
Background Chloroplast is an essential organelle in plants which contains independent
genome. Chloroplast genomes have been widely used for plant phylogenetic inference …

The complete chloroplast genome of ornamental coffee tree, Coffea arabica L. (Rubiaceae)

J Park, Y Kim, H Xi, KI Heo - Mitochondrial DNA Part B, 2019 - Taylor & Francis
Coffea arabica L. taking 70% of world coffee production is also used as an ornamental
species. One imported coffee tree from Indonesia near to thirty years ago of which leaf is …

Assembly, annotation and analysis of chloroplast genomes

X Zhong - 2020 - research-repository.uwa.edu.au
Chloroplast genome data is useful for phylogenetic analyses, for species identification and
for tracing evolutionary adaptations. Current sequencing technology enables us to obtain …

Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

K Kahraman, SJ Lucas - Bmc Genomics, 2019 - Springer
Background Several bioinformatics tools have been designed for assembly and annotation
of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable …

A systematic comparison of chloroplast genome assembly tools

JA Freudenthal, S Pfaff, N Terhoeven, A Korte… - Genome Biology, 2020 - Springer
Background Chloroplasts are intracellular organelles that enable plants to conduct
photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an …

Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution

W Martin, O Deusch, N Stawski, N Grünheit… - Trends in plant …, 2005 - cell.com
The traditional approach to plant molecular phylogenetics involves amplifying, sequencing
and analyzing one or a few genes from many species and is conducive to broad taxon …

CPGView: A package for visualizing detailed chloroplast genome structures

S Liu, Y Ni, J Li, X Zhang, H Yang… - Molecular ecology …, 2023 - Wiley Online Library
Chloroplast genomes have been widely used in studying plant phylogeny and evolution.
Several chloroplast genome visualization tools have been developed to display the …

An update on chloroplast genomes

V Ravi, JP Khurana, AK Tyagi, P Khurana - Plant systematics and …, 2008 - Springer
Plant cells possess two more genomes besides the central nuclear genome: the
mitochondrial genome and the chloroplast genome (or plastome). Compared to the gigantic …

Development of a reference standard library of chloroplast genome sequences, GenomeTrakrCP

N Zhang, P Ramachandran, J Wen, JA Duke… - Planta …, 2017 - thieme-connect.com
Precise, species-level identification of plants in foods and dietary supplements is difficult.
While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has …