Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae)
Open Access
- 9 June 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 22 (1), 1-13
- https://doi.org/10.1186/s12864-021-07769-x
Abstract
Background: Crape myrtles, belonging to the genus Lagerstroemia L., have beautiful paniculate inflorescences and are cultivated as important ornamental tree species for landscaping and gardening. However, the phylogenetic relationships within Lagerstroemia have remained unresolved likely caused by limited sampling and the insufficient number of informative sites used in previous studies. Results: In this study, we sequenced 20 Lagerstroemia chloroplast genomes and combined with 15 existing chloroplast genomes from the genus to investigate the phylogenetic relationships and divergence times within Lagerstroemia. The phylogenetic results indicated that this genus is a monophyletic group containing four clades. Our dating analysis suggested that Lagerstroemia originated in the late Paleocene (~ 60 Ma) and started to diversify in the middle Miocene. The diversification of most species occurred during the Pleistocene. Four variable loci, trnD-trnY-trnE, rrn16-trnI, ndhF-rpl32-trnL and ycf1, were discovered in the Lagerstroemia chloroplast genomes. Conclusions: The chloroplast genome information was successfully utilized for molecular characterization of diverse crape myrtle samples. Our results are valuable for the global genetic diversity assessment, conservation and utilization of Lagerstroemia.Funding Information
- National Natural Science Foundation of Chin (31770744)
- Fundamental Research Funds for the Central Universities (BLX201932)
This publication has 47 references indexed in Scilit:
- 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
- Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA BarcodingPLOS ONE, 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
- Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare IIIAmerican Journal of Botany, 2007
- Phylogenetic Analysis of the Lythraceae Based on Four Gene Regions and MorphologyInternational Journal of Plant Sciences, 2005
- Comparison of the Tertiary flora of southwest China and northeast India and its significance in the antiquity of the modern Himalayan floraReview of Palaeobotany and Palynology, 2005
- Phylogenetics of Lythraceaesensu lato: A Preliminary Analysis Based on ChloroplastrbcL Gene,psaA‐ycf3Spacer, and Nuclear rDNA Internal Transcribed Spacer (ITS) SequencesInternational Journal of Plant Sciences, 2002
- Zwei neue Arten von Samen aus dem deutschen JungtertiärFeddes Repertorium, 1996