The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis
Open Access
- 1 December 2020
- Vol. 9 (12), 1692
- https://doi.org/10.3390/plants9121692
Abstract
Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.Keywords
This publication has 67 references indexed in Scilit:
- OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data setsNucleic Acids Research, 2013
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution, 2013
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of Computational Biology, 2012
- Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence dataBioinformatics, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Analysis and Functional Prediction of Reactive Cysteine ResiduesJournal of Biological Chemistry, 2012
- MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model SpaceSystematic Biology, 2012
- BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical PhylogeneticsSystematic Biology, 2011
- The evolution of the plastid chromosome in land plants: gene content, gene order, gene functionPlant Molecular Biology, 2011
- Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence AlignmentsSystematic Biology, 2007