Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)

Wenpan Dong; Chao Xu; Delu Li; Xiaobai Jin; Ruili Li; Qi Lu; Zhili Suo

doi:10.7717/peerj.2699

Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)

PeerJ. 2016 Nov 10:4:e2699. doi: 10.7717/peerj.2699. eCollection 2016.

Authors

Wenpan Dong¹, Chao Xu², Delu Li³, Xiaobai Jin⁴, Ruili Li⁴, Qi Lu⁵, Zhili Suo⁶

Affiliations

¹ State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
² State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
³ Gansu Desert Control Research Institute , Gansu , China.
⁴ Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing , China.
⁵ Institute of Desertification Studies, Chinese Academy of Forestry , Beijing , China.
⁶ State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing , China.

Abstract

The Haloxylon genus 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 of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp 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. Each Haloxylon cp 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 the petA-psbJ intergenic region and rpl16 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 on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.

Keywords: Amaranthaceae; Chloroplast genome; Evolution; Haloxylon; Psammophytes; Structure.

Grants and funding

This study was financially supported by the China National Science and Technology Plan Project (2012BAD16B0101), the “948 Program” (No. 2008-4-47), the Identification and Screening of Haloxylon Germplasm Resources (80117B1001), the State Forestry Administration “Public Welfare Research Foundation” (No. 201004010), the Scientific and Technological Support Project from the Chinese Ministry of Science and Technology (2006BAD26B0101), the National Natural Science Foundation of China (No. 30972412), the joint projects No. 70009C1020 and 70009C1036, and the National Forest Genetic Resources Platform (2005DKA21003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.