Comparative analysis of the complete chloroplast genome sequences in psammophyticHaloxylonspecies (Amaranthaceae)

Wenpan Dong, Chao Xu, Delu Li, Xiaobai Jin, Ruili Li, Qi Lu, Zhili Suo
2016 PeerJ  
TheHaloxylongenus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes ofHaloxylon ammodendron(HA) andHaloxylon persicum(HP) and conducted comparative genomic analyses on these and two other
more » ... sentative Amaranthaceae species. Similar to other higher plants, we found that theHaloxyloncp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. EachHaloxyloncp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in thepetA-psbJ intergenic region andrpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies onHaloxylongenetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.
doi:10.7717/peerj.2699 pmid:27867769 pmcid:PMC5111891 fatcat:j7bgi5c2zzac7hsj4hwpcfmfgm