Abstract
Among the four species of Echinacanthus (Acanthaceae), one distributed in the West Himalayan region and three restricted to the Sino-Vietnamese karst region. Because of its ecological significance, molecular markers are necessary for proper assessment of its genetic diversity and phylogenetic relationships. Herein, the complete chloroplast genomes of four Echinacanthus species were determined for the first time. The results indicated that all the chloroplast genomes were mapped as a circular structure and each genomes included 113 unique genes, of which 80 were protein-coding, 29 were tRNAs, and 4 were rRNAs. However, the four cp genomes ranged from 151,333 to 152,672 bp in length. Comparison of the four cp genomes showed that the divergence level was greater between geographic groups. We also analyzed IR expansion or contraction in the four cp genomes and the fifth type of the large single copy/inverted repeat region in Lamiales was suggested. Furthermore, based on the analyses of comparison and nucleotide variability, six most divergent sequences (rrn16, ycf1, ndhA, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, and psaA-ycf3) were identified. A total of 37–45 simple sequence repeats were discovered in the four species and 22 SSRs were identified as candidate effective molecular markers for detecting interspecies polymorphisms. These SSRs and hotspot regions could be used as potential molecular markers for future study. Phylogenetic analysis based on Bayesian and parsimony methods did not support the monophyly of Echinacanthus. The phylogenetic relationships among the four species were clearly resolved and the results supported the recognition of the Sino-Vietnamese Echinacanthus species as a new genus. Based on the protein sequence evolution analysis, 12 genes (rpl14, rpl16, rps4, rps15, rps18, rps19, psbK, psbN, ndhC, ndhJ, rpoB, and infA) were detected under positive selection in branch of Sino-Vietnamese Echinacanthus species. These genes will lead to understanding the adaptation of Echinacanthus species to karst environment. The study will help to resolve the phylogenetic relationship and understand the adaptive evolution of Echinacanthus. It will also provide genomic resources and potential markers suitable for future species identification and speciation studies of the genus.
Highlights
The complete chloroplast genomes of the four species of Echinacanthus ranged from 151,333 bp (E. lofouensis) to Echinacanthus longipes Echinacanthus lofouensis
The size of the genome ranged from 151,333 (E. lofouensis) to 152,672 bp (E. attenuatus), which was longer than the genomes of A. paniculata (Ding et al, 2016), R. breedlovei, and S. cusia (Chen et al, 2018)
Rps12 in Echinacanthus was recognized as the trans-spliced gene, which was in line with observations in other species (Hildebrand et al, 1988; Liu et al, 2016; Gichira et al, 2017; Chen et al, 2018)
Summary
Echinacanthus Nees is a small genus in the tribe Ruellieae of the family Acanthaceae typified by E. attenuatus Nees (Nees Von Esenbeck, 1832; Anderson, 1867; Bentham, 1876; Bremekamp, 1965; Scotland and Vollesen, 2000; Deng et al, 2010; Hu et al, 2011; Tripp et al, 2013). Four species, E. attenuatus, E. longipes, E. longzhouensis and E. lofouensis, are recognized in the genus (Deng et al, 2010; Hu et al, 2011; Tripp et al, 2013). Previous studies did not appear to fully resolve the phylogenetic relationship of Echinacanthus
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