Journal
INDUSTRIAL CROPS AND PRODUCTS
Volume 162, Issue -, Pages -Publisher
ELSEVIER
DOI: 10.1016/j.indcrop.2021.113248
Keywords
Miscanthus species; Chloroplast genome; Multiple comparison; Structural changes; Phylogenomics; Taxonomic identification
Categories
Funding
- National Natural Science Foundation of China [31571740, 31371691]
- National High-tech RD Program [2012AA101801]
- Natural Science Foundation of Hubei Province [2013CFA103]
- Natural Science Foundation of the Jiangsu Higher Education Institutions of China [19KJB180023]
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The chloroplast genomes of five Miscanthus species were sequenced using Illumina technology, revealing conservation in gene content and order but also identifying variation hotspots. Comparisons with other grass chloroplast genomes showed polymorphism hotspots, while phylogenetic analysis suggested a sister relationship between certain clades. This comprehensive analysis provides valuable genetic information for phylogeography, population genetics, and plastid genetic engineering research in Miscanthus.
Background: Miscanthus has been considered as potentially high-yielding biomass crop with the low-nutrient requirements, high capability of Carbon mitigation and water-use efficiency. Miscanthus species have restricted to investigate functional genomics of their large genome size, which leads to challenges to genomicsaided crop improvement. Sequencing of the plastid genomes of Miscanthus is one of complementary tool making it available for genetic researches. Results: The complete chloroplast (cp) genomes of five Miscanthus species were sequenced using Illumina sequencing. Comparisons between the five chloroplast genome sequences revealed their conservation in gene content and order, including the IR/SC boundaries. However, some hotspots in coding regions and intergenic regions also occurred. Specifically a 13 bp deletion in the intergenic region of rps16-trnQ and a 17 bp deletion in rps4-trnT are shared by Miscanthus lutarioriparius L., Miscanthus sacchariflorus N. and Miscanthus x giganteus. In addition, a 39 bp deletion in trnL-trnF is shared by Miscanthus sinensis A. and Miscanthus floridulus W.. Comparisons of complete chloroplast genome of Miscanthus lutarioriparius to five published grass chloroplast genomes also reveal several hotspot regions with high polymorphism. Phylogenetic analysis based on complete chloroplast genomes and coding sequences of 77 protein genes suggest a sister relationship between the Eumiscanthus clade and the Triarrhena clade. Conclusions: This report is the first comprehensive comparative analyses on Miscanthus species cp genome combining other published grass chloroplast genomes. The availability of these results will supplement valuable genetic information and framework for further phylogeography, population genetics and plastid genetic engineering researches in Miscanthus.sp.
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