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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
Phylogenomic and evolutionary analysis of arrowhead (Sagittaria L.) chloroplast genomes
Weiwei Zhao1, Feng Gao2, Yiling Wei2,3
1College of Biology and Chemistry, Minzu Normal University of Xingyi, Xingyi 562400, China.
Abstract:
This study employed high-throughput sequencing to assemble and annotate the complete chloroplast genomes of three Sagittaria species. These genomes showed a conserved quadripartite structure, with length (∼178,339 bp) and GC content (36.8%-36.9%) exceeding those of other Alismataceae genera. Comparative analysis revealed structural conservation but species-specific variations at the JLB and JSA junctions. We identified numerous SNPs and SSRs across five species and found the rps16 gene and trnT-trnL spacer to be hypervariable, suggesting them as molecular markers. Codon usage bias indicated limited mutational pressure. Selective pressure analysis detected positive selection in clpP and ycf2. Phylogenetic analysis strongly supported Caldesia as sister to Sagittaria and placed S. platyphylla basally. Divergence time estimation suggested that Sagittaria and Caldesia split approximately 23.53 million years ago (Mya), while the internal diversification of Sagittaria occurred around 4.82 Mya. Our findings provide invaluable genomic resources and deep insights into the evolution, systematics, and potential genetic improvement of Sagittaria, which has significant ecological and industrial applications.
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