Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide
Typha is a cosmopolitan aquatic plant genus that includes species with widespread global distributions. In previous studies, a revised molecular phylogeny was inferred using seven plastid loci from nine Typha species across different geographic regions. By utilizing complete organellar genomes, we a...
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Frontiers Media S.A.
2024-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1484531/full |
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| author | Thida Soe Jiali Kong Jiali Kong Liyun Nie Liyun Nie Jie Wang Jie Wang Dan Peng Luke R. Tembrock Zhiqiang Wu |
| author_facet | Thida Soe Jiali Kong Jiali Kong Liyun Nie Liyun Nie Jie Wang Jie Wang Dan Peng Luke R. Tembrock Zhiqiang Wu |
| author_sort | Thida Soe |
| collection | DOAJ |
| description | Typha is a cosmopolitan aquatic plant genus that includes species with widespread global distributions. In previous studies, a revised molecular phylogeny was inferred using seven plastid loci from nine Typha species across different geographic regions. By utilizing complete organellar genomes, we aim to provide a more comprehensive dataset that offers a robust phylogenetic signal for resolving Typha species evolutionary relationships. Here, we assembled T. latifolia and T. domingensis mitochondrial genomes (mitogenomes) using a combination of short-read and long-read data (PacBio, ONT). The mitogenomes of both species are assembled into single circular molecules of 395,136 bp and 395,140 bp in length, respectively, with a similar GC content of 46.7%. A total of 39 protein-coding genes, 17 tRNA genes, and 3 rRNA genes were annotated in both mitogenomes. The plastid genomes (plastomes) of both species possess typical quadripartite structures observed across most plants, with sizes of 161,545 bp and 161,230 bp. The overall average GC content of the plastomes of both species was 36.6%. The comparative analysis of the plastome and mitogenome revealed that 12 mitogenome DNA fragments share similar sequences with in the repeat regions of the corresponding plastomes, suggesting a past transfer of repeat regions into the mitogenome. Additionally, the mitogenomes of the two Typha species exhibited high sequence conservation with several syntenic blocks. Phylogenetic analysis of the organellar genomes of the two Typha species and 10 related species produced congruent phylogenetic trees. The availability of these organellar genomes from two Typha species provide valuable genetic resources for studying the evolution of Typhaceae and will improve taxonomic classifications within the family. |
| format | Article |
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| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-dd2a3f6427a74585aa97a76d652f3e9b2024-12-05T04:26:22ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-12-011510.3389/fpls.2024.14845311484531Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwideThida Soe0Jiali Kong1Jiali Kong2Liyun Nie3Liyun Nie4Jie Wang5Jie Wang6Dan Peng7Luke R. Tembrock8Zhiqiang Wu9Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, ChinaShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaSchool of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA, AustraliaShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaSchool of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA, AustraliaCollege of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, ChinaDepartment of Agricultural Biology, Colorado State University, Fort Collins, CO, United StatesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaTypha is a cosmopolitan aquatic plant genus that includes species with widespread global distributions. In previous studies, a revised molecular phylogeny was inferred using seven plastid loci from nine Typha species across different geographic regions. By utilizing complete organellar genomes, we aim to provide a more comprehensive dataset that offers a robust phylogenetic signal for resolving Typha species evolutionary relationships. Here, we assembled T. latifolia and T. domingensis mitochondrial genomes (mitogenomes) using a combination of short-read and long-read data (PacBio, ONT). The mitogenomes of both species are assembled into single circular molecules of 395,136 bp and 395,140 bp in length, respectively, with a similar GC content of 46.7%. A total of 39 protein-coding genes, 17 tRNA genes, and 3 rRNA genes were annotated in both mitogenomes. The plastid genomes (plastomes) of both species possess typical quadripartite structures observed across most plants, with sizes of 161,545 bp and 161,230 bp. The overall average GC content of the plastomes of both species was 36.6%. The comparative analysis of the plastome and mitogenome revealed that 12 mitogenome DNA fragments share similar sequences with in the repeat regions of the corresponding plastomes, suggesting a past transfer of repeat regions into the mitogenome. Additionally, the mitogenomes of the two Typha species exhibited high sequence conservation with several syntenic blocks. Phylogenetic analysis of the organellar genomes of the two Typha species and 10 related species produced congruent phylogenetic trees. The availability of these organellar genomes from two Typha species provide valuable genetic resources for studying the evolution of Typhaceae and will improve taxonomic classifications within the family.https://www.frontiersin.org/articles/10.3389/fpls.2024.1484531/fullorganellar genomesphylogenycomparative analysisTyphasynteny |
| spellingShingle | Thida Soe Jiali Kong Jiali Kong Liyun Nie Liyun Nie Jie Wang Jie Wang Dan Peng Luke R. Tembrock Zhiqiang Wu Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide Frontiers in Plant Science organellar genomes phylogeny comparative analysis Typha synteny |
| title | Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide |
| title_full | Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide |
| title_fullStr | Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide |
| title_full_unstemmed | Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide |
| title_short | Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide |
| title_sort | organelle genome assembly annotation and comparative analyses of typha latifolia and t domingensis two keystone species for wetlands worldwide |
| topic | organellar genomes phylogeny comparative analysis Typha synteny |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1484531/full |
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