Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)
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 u...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2016-11-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/2699.pdf |
| _version_ | 1797417690345766912 |
|---|---|
| author | Wenpan Dong Chao Xu Delu Li Xiaobai Jin Ruili Li Qi Lu Zhili Suo |
| author_facet | Wenpan Dong Chao Xu Delu Li Xiaobai Jin Ruili Li Qi Lu Zhili Suo |
| author_sort | Wenpan Dong |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T06:23:13Z |
| format | Article |
| id | doaj.art-dd0daf76f9804305af07b15eef13f5da |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:23:13Z |
| publishDate | 2016-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-dd0daf76f9804305af07b15eef13f5da2023-12-03T11:33:56ZengPeerJ Inc.PeerJ2167-83592016-11-014e269910.7717/peerj.2699Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)Wenpan Dong0Chao Xu1Delu Li2Xiaobai Jin3Ruili Li4Qi Lu5Zhili Suo6State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, ChinaGansu Desert Control Research Institute, Gansu, ChinaBeijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, ChinaBeijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, ChinaInstitute of Desertification Studies, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, ChinaThe 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.https://peerj.com/articles/2699.pdfChloroplast genomePsammophytesStructureEvolutionAmaranthaceaeHaloxylon |
| spellingShingle | Wenpan Dong Chao Xu Delu Li Xiaobai Jin Ruili Li Qi Lu Zhili Suo Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) PeerJ Chloroplast genome Psammophytes Structure Evolution Amaranthaceae Haloxylon |
| title | Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) |
| title_full | Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) |
| title_fullStr | Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) |
| title_full_unstemmed | Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) |
| title_short | Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) |
| title_sort | comparative analysis of the complete chloroplast genome sequences in psammophytic haloxylon species amaranthaceae |
| topic | Chloroplast genome Psammophytes Structure Evolution Amaranthaceae Haloxylon |
| url | https://peerj.com/articles/2699.pdf |
| work_keys_str_mv | AT wenpandong comparativeanalysisofthecompletechloroplastgenomesequencesinpsammophytichaloxylonspeciesamaranthaceae AT chaoxu comparativeanalysisofthecompletechloroplastgenomesequencesinpsammophytichaloxylonspeciesamaranthaceae AT deluli comparativeanalysisofthecompletechloroplastgenomesequencesinpsammophytichaloxylonspeciesamaranthaceae AT xiaobaijin comparativeanalysisofthecompletechloroplastgenomesequencesinpsammophytichaloxylonspeciesamaranthaceae AT ruilili comparativeanalysisofthecompletechloroplastgenomesequencesinpsammophytichaloxylonspeciesamaranthaceae AT qilu comparativeanalysisofthecompletechloroplastgenomesequencesinpsammophytichaloxylonspeciesamaranthaceae AT zhilisuo comparativeanalysisofthecompletechloroplastgenomesequencesinpsammophytichaloxylonspeciesamaranthaceae |