An improved method for chloroplast genome sequencing in non-model forest tree species

FK Du, T Lang, S Lu, Y Wang, J Li, K Yin - Tree genetics & genomes, 2015 - Springer
Chloroplast genomes can provide a large amount of information and resources for use in
studies on plant evolution and molecular ecology. However, a rapid and efficient method for …

Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs

JB Yang, DZ Li, HT Li - Molecular ecology resources, 2014 - Wiley Online Library
Chloroplast genomes supply indispensable information that helps improve the phylogenetic
resolution and even as organelle‐scale barcodes. Next‐generation sequencing …

Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus

S Senthilkumar, K Ulaganathan, M Ghosh Dasgupta - 3 Biotech, 2021 - Springer
Chloroplast genome sequencing is an essential tool to understand genome evolution and
phylogenetic relationship. The available methods for constructing chloroplast genome …

Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs

T Zhang, CX Zeng, JB Yang, HT Li… - Journal of Systematics …, 2016 - Wiley Online Library
Chloroplast genome information helps improve the phylogenetic resolution and can act as
organelle‐scale barcodes in recently radiated plant groups. Previously we reported that nine …

Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq

C Osuna-Mascaró, R Rubio de Casas, F Perfectti - Scientific reports, 2018 - nature.com
Chloroplast genomes (cp genomes) are widely used in comparative genomics, population
genetics, and phylogenetic studies. Obtaining chloroplast genomes from RNA-Seq data …

Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform

RA Atherton, BJ McComish, LD Shepherd, LA Berry… - Plant methods, 2010 - Springer
Background Complete chloroplast genome sequences provide a valuable source of
molecular markers for studies in molecular ecology and evolution of plants. To obtain …

Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

H Zhou, X Gao, K Woeste, P Zhao, S Zhang - Forests, 2021 - mdpi.com
Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of
species and reconstructing phylogenetic relationships in plants. Species of the genus …

Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management

LW Alexander, KE Woeste - Tree Genetics & Genomes, 2014 - Springer
Given the low intraspecific chloroplast diversity detected in northern red oak (Quercus rubra
L.), more powerful genetic tools are necessary to accurately characterize Q. rubra …

De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA …

S Izan, D Esselink, RGF Visser… - Frontiers in Plant …, 2017 - frontiersin.org
Whole Genome Shotgun (WGS) sequences of plant species often contain an abundance of
reads that are derived from the chloroplast genome. Up to now these reads have generally …

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

W Wang, M Schalamun, A Morales-Suarez, D Kainer… - BMC genomics, 2018 - Springer
Background Chloroplasts are organelles that conduct photosynthesis in plant and algal
cells. The information chloroplast genome contained is widely used in agriculture and …