Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution

K Fučíková, PO Lewis, LA Lewis - Molecular Phylogenetics and Evolution, 2016 - Elsevier
Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With
the increasing availability of complete chloroplast genome sequences, the opportunity …

[HTML][HTML] Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

Q Liu, X Li, M Li, W Xu, T Schwarzacher… - BMC plant biology, 2020 - Springer
Abstract Background Oat (Avena sativa L.) is a recognized health-food, and the contributions
of its different candidate A-genome progenitor species remain inconclusive. Here, we report …

[HTML][HTML] Comparative Chloroplast Genomes of Camellia Species

JB Yang, SX Yang, HT Li, J Yang, DZ Li - PLoS One, 2013 - journals.plos.org
Background Camellia, comprising more than 200 species, is a valuable economic
commodity due to its enormously popular commercial products: tea leaves, flowers, and high …

[HTML][HTML] Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis

S Asaf, AL Khan, MA Khan, M Waqas, SM Kang… - Scientific reports, 2017 - nature.com
We investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri
ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to …

Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications

VV Goremykin, B Holland… - Molecular biology …, 2005 - academic.oup.com
Determining the phylogenetic relationships among the major lines of angiosperms is a long-
standing problem, yet the uncertainty as to the phylogenetic affinity of these lines persists …

[HTML][HTML] The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in …

LA Cauz-Santos, CF Munhoz, N Rodde… - Frontiers in Plant …, 2017 - frontiersin.org
The family Passifloraceae consists of some 700 species classified in around 16 genera.
Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit …

[HTML][HTML] 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 …

Complete chloroplast genome sequence of pineapple (Ananas comosus)

K Nashima, S Terakami, C Nishitani, M Kunihisa… - Tree Genetics & …, 2015 - Springer
Since chloroplasts are maternally inherited and have unique features in evolution, their
genome sequences have been broadly used in phylogenetic studies of plants. Here, we …

[HTML][HTML] 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 …

[HTML][HTML] Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

H Huang, C Shi, Y Liu, SY Mao, LZ Gao - BMC Evolutionary biology, 2014 - Springer
Background Camellia is an economically and phylogenetically important genus in the family
Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and …