Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic Analysis
High genetic diversity and low differentiation present challenges in taxonomy and systematics of <i>Salix</i>. Chloroplast (cp) genome sequencing is efficient for providing new genomic information and elucidating phylogenetic relationships. <i>Salix spathulifolia</i> Seemen,...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-12-01
|
| Series: | Forests |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4907/12/12/1681 |
| _version_ | 1797504659305267200 |
|---|---|
| author | Xue-Jiao Zhang Kang-Jia Liu Ya-Chao Wang Jian He Yuan-Mi Wu Zhi-Xiang Zhang |
| author_facet | Xue-Jiao Zhang Kang-Jia Liu Ya-Chao Wang Jian He Yuan-Mi Wu Zhi-Xiang Zhang |
| author_sort | Xue-Jiao Zhang |
| collection | DOAJ |
| description | High genetic diversity and low differentiation present challenges in taxonomy and systematics of <i>Salix</i>. Chloroplast (cp) genome sequencing is efficient for providing new genomic information and elucidating phylogenetic relationships. <i>Salix spathulifolia</i> Seemen, <i>S. cupularis</i> Rehder, and <i>S. annulifera</i> C.Marquand & Airy Shaw are three shrubby willows spread in high-altitude regions in western China. In this study, the integrated circular cp genomes were sequenced and analyzed, and a phylogeny of <i>Salix</i> was constructed on the basis of the cp genomes. The results of chloroplast assembly and annotation information were used to characterize genome feature and interspecific variation. The phylogenetic position of the three willows was evaluated using phylogenetic analysis. Full-length cp genomes were 155,566–155,680 bp with a typical double-stranded circular quadripartite structure, containing one large single-copy region (LSC, 84,431–4552 bp), one small single-copy region (SSC: 16,206–16,221 bp), and two inverted repeats (IR: 27,453–27,461 bp). The cp genomes encoded 130 genes, including 8 rRNA genes, 37 tRNA genes, and 85 protein-coding genes. The guanine-cytosine (GC) content of the overall genome was 36.7%. Comparison among the three willows’ cp genomes revealed high similarity. Phylogenetic analysis indicated that <i>S. spathulifolia</i> was a basal taxon of clade I, while <i>S. annulifera</i> formed a monophyletic group with <i>S. rorida</i> Laksch.; <i>S. cupularis</i> was sister to <i>S. suchowensis</i> W.C. Cheng and <i>S. psammophila</i> Z. Wang & Chang Y. Yang. The complete chloroplast genomes of the three willows provides an additional sequence-based resource for studying the phylogeny and evolutionary history of Salicaceae. |
| first_indexed | 2024-03-10T04:07:32Z |
| format | Article |
| id | doaj.art-ba32376d39f74af4a55720b772f58062 |
| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-10T04:07:32Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-ba32376d39f74af4a55720b772f580622023-11-23T08:20:54ZengMDPI AGForests1999-49072021-12-011212168110.3390/f12121681Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic AnalysisXue-Jiao Zhang0Kang-Jia Liu1Ya-Chao Wang2Jian He3Yuan-Mi Wu4Zhi-Xiang Zhang5Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature, Conservation, Beijing Forestry University, Beijing 100083, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature, Conservation, Beijing Forestry University, Beijing 100083, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature, Conservation, Beijing Forestry University, Beijing 100083, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature, Conservation, Beijing Forestry University, Beijing 100083, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature, Conservation, Beijing Forestry University, Beijing 100083, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature, Conservation, Beijing Forestry University, Beijing 100083, ChinaHigh genetic diversity and low differentiation present challenges in taxonomy and systematics of <i>Salix</i>. Chloroplast (cp) genome sequencing is efficient for providing new genomic information and elucidating phylogenetic relationships. <i>Salix spathulifolia</i> Seemen, <i>S. cupularis</i> Rehder, and <i>S. annulifera</i> C.Marquand & Airy Shaw are three shrubby willows spread in high-altitude regions in western China. In this study, the integrated circular cp genomes were sequenced and analyzed, and a phylogeny of <i>Salix</i> was constructed on the basis of the cp genomes. The results of chloroplast assembly and annotation information were used to characterize genome feature and interspecific variation. The phylogenetic position of the three willows was evaluated using phylogenetic analysis. Full-length cp genomes were 155,566–155,680 bp with a typical double-stranded circular quadripartite structure, containing one large single-copy region (LSC, 84,431–4552 bp), one small single-copy region (SSC: 16,206–16,221 bp), and two inverted repeats (IR: 27,453–27,461 bp). The cp genomes encoded 130 genes, including 8 rRNA genes, 37 tRNA genes, and 85 protein-coding genes. The guanine-cytosine (GC) content of the overall genome was 36.7%. Comparison among the three willows’ cp genomes revealed high similarity. Phylogenetic analysis indicated that <i>S. spathulifolia</i> was a basal taxon of clade I, while <i>S. annulifera</i> formed a monophyletic group with <i>S. rorida</i> Laksch.; <i>S. cupularis</i> was sister to <i>S. suchowensis</i> W.C. Cheng and <i>S. psammophila</i> Z. Wang & Chang Y. Yang. The complete chloroplast genomes of the three willows provides an additional sequence-based resource for studying the phylogeny and evolutionary history of Salicaceae.https://www.mdpi.com/1999-4907/12/12/1681<i>Salix</i>chloroplast genomesequence variationcomparative analysisphylogeny |
| spellingShingle | Xue-Jiao Zhang Kang-Jia Liu Ya-Chao Wang Jian He Yuan-Mi Wu Zhi-Xiang Zhang Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic Analysis Forests <i>Salix</i> chloroplast genome sequence variation comparative analysis phylogeny |
| title | Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic Analysis |
| title_full | Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic Analysis |
| title_fullStr | Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic Analysis |
| title_full_unstemmed | Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic Analysis |
| title_short | Complete Chloroplast Genomes of Three <i>Salix</i> Species: Genome Structures and Phylogenetic Analysis |
| title_sort | complete chloroplast genomes of three i salix i species genome structures and phylogenetic analysis |
| topic | <i>Salix</i> chloroplast genome sequence variation comparative analysis phylogeny |
| url | https://www.mdpi.com/1999-4907/12/12/1681 |
| work_keys_str_mv | AT xuejiaozhang completechloroplastgenomesofthreeisalixispeciesgenomestructuresandphylogeneticanalysis AT kangjialiu completechloroplastgenomesofthreeisalixispeciesgenomestructuresandphylogeneticanalysis AT yachaowang completechloroplastgenomesofthreeisalixispeciesgenomestructuresandphylogeneticanalysis AT jianhe completechloroplastgenomesofthreeisalixispeciesgenomestructuresandphylogeneticanalysis AT yuanmiwu completechloroplastgenomesofthreeisalixispeciesgenomestructuresandphylogeneticanalysis AT zhixiangzhang completechloroplastgenomesofthreeisalixispeciesgenomestructuresandphylogeneticanalysis |