Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales
Abstract Background Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45;...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-06-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-019-1870-3 |
| _version_ | 1818884207346188288 |
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| author | Cuihua Gu Li Ma Zhiqiang Wu Kai Chen Yixiang Wang |
| author_facet | Cuihua Gu Li Ma Zhiqiang Wu Kai Chen Yixiang Wang |
| author_sort | Cuihua Gu |
| collection | DOAJ |
| description | Abstract Background Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45; Nesaea, with 50; Lagerstroemia, with 56; and Cuphea, with 275 species. Results We reported six newly sequenced chloroplast (cp) genomes (Duabanga grandiflora, Trapa natans, Lythrum salicaria, Lawsonia inermis, Woodfordia fruticosa and Rotala rotundifolia) and compared them with 16 other cp genomes of Lythraceae species. The cp genomes of the 22 Lythraceae species ranged in length from 152,049 bp to 160,769 bp. In each Lythraceae species, the cp genome contained 112 genes consisting of 78 protein coding genes, four ribosomal RNAs and 30 transfer RNAs. Furthermore, we detected 211–332 simple sequence repeats (SSRs) in six categories and 7–27 long repeats in four categories. We selected ten divergent hotspots (ndhF, matK, ycf1, rpl22, rpl32, trnK-rps16, trnR-atpA, rpl32-trnL, trnH-psbA and trnG-trnR) among the 22 Lythraceae species to be potential molecular markers. We constructed phylogenetic trees from 42 Myrtales plants with 8 Geraniales plants as out groups. The relationships among the Myrtales species were effectively distinguished by maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) trees constructed using 66 protein coding genes. Generally, the 22 Lythraceae species gathered into one clade, which was resolved as sister to the three Onagraceae species. Compared with Melastomataceae and Myrtaceae, Lythraceae and Onagraceae differentiated later within Myrtales. Conclusions The study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study. |
| first_indexed | 2024-12-19T15:45:53Z |
| format | Article |
| id | doaj.art-f49be8729ab64007bab0f4d99f540de8 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-19T15:45:53Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-f49be8729ab64007bab0f4d99f540de82022-12-21T20:15:21ZengBMCBMC Plant Biology1471-22292019-06-0119111910.1186/s12870-019-1870-3Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within MyrtalesCuihua Gu0Li Ma1Zhiqiang Wu2Kai Chen3Yixiang Wang4School of Landscape and Architecture, Zhejiang A&F UniversitySchool of Landscape and Architecture, Zhejiang A&F UniversityDepartment of Biology, Colorado State UniversitySchool of Landscape and Architecture, Zhejiang A&F UniversitySchool of Environment and Resources, Zhejiang A&F UniversityAbstract Background Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45; Nesaea, with 50; Lagerstroemia, with 56; and Cuphea, with 275 species. Results We reported six newly sequenced chloroplast (cp) genomes (Duabanga grandiflora, Trapa natans, Lythrum salicaria, Lawsonia inermis, Woodfordia fruticosa and Rotala rotundifolia) and compared them with 16 other cp genomes of Lythraceae species. The cp genomes of the 22 Lythraceae species ranged in length from 152,049 bp to 160,769 bp. In each Lythraceae species, the cp genome contained 112 genes consisting of 78 protein coding genes, four ribosomal RNAs and 30 transfer RNAs. Furthermore, we detected 211–332 simple sequence repeats (SSRs) in six categories and 7–27 long repeats in four categories. We selected ten divergent hotspots (ndhF, matK, ycf1, rpl22, rpl32, trnK-rps16, trnR-atpA, rpl32-trnL, trnH-psbA and trnG-trnR) among the 22 Lythraceae species to be potential molecular markers. We constructed phylogenetic trees from 42 Myrtales plants with 8 Geraniales plants as out groups. The relationships among the Myrtales species were effectively distinguished by maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) trees constructed using 66 protein coding genes. Generally, the 22 Lythraceae species gathered into one clade, which was resolved as sister to the three Onagraceae species. Compared with Melastomataceae and Myrtaceae, Lythraceae and Onagraceae differentiated later within Myrtales. Conclusions The study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study.http://link.springer.com/article/10.1186/s12870-019-1870-3LythraceaeChloroplast genomePhylogenomicMyrtales |
| spellingShingle | Cuihua Gu Li Ma Zhiqiang Wu Kai Chen Yixiang Wang Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales BMC Plant Biology Lythraceae Chloroplast genome Phylogenomic Myrtales |
| title | Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales |
| title_full | Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales |
| title_fullStr | Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales |
| title_full_unstemmed | Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales |
| title_short | Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales |
| title_sort | comparative analyses of chloroplast genomes from 22 lythraceae species inferences for phylogenetic relationships and genome evolution within myrtales |
| topic | Lythraceae Chloroplast genome Phylogenomic Myrtales |
| url | http://link.springer.com/article/10.1186/s12870-019-1870-3 |
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