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Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
BACKGROUND: As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attr...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830136/ https://www.ncbi.nlm.nih.gov/pubmed/35139817 http://dx.doi.org/10.1186/s12864-022-08336-8 |
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author | Sielemann, Katharina Pucker, Boas Schmidt, Nicola Viehöver, Prisca Weisshaar, Bernd Heitkam, Tony Holtgräwe, Daniela |
author_facet | Sielemann, Katharina Pucker, Boas Schmidt, Nicola Viehöver, Prisca Weisshaar, Bernd Heitkam, Tony Holtgräwe, Daniela |
author_sort | Sielemann, Katharina |
collection | PubMed |
description | BACKGROUND: As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. RESULTS: We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. CONCLUSION: In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08336-8. |
format | Online Article Text |
id | pubmed-8830136 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-88301362022-02-11 Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives Sielemann, Katharina Pucker, Boas Schmidt, Nicola Viehöver, Prisca Weisshaar, Bernd Heitkam, Tony Holtgräwe, Daniela BMC Genomics Research BACKGROUND: As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. RESULTS: We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. CONCLUSION: In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08336-8. BioMed Central 2022-02-10 /pmc/articles/PMC8830136/ /pubmed/35139817 http://dx.doi.org/10.1186/s12864-022-08336-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Sielemann, Katharina Pucker, Boas Schmidt, Nicola Viehöver, Prisca Weisshaar, Bernd Heitkam, Tony Holtgräwe, Daniela Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives |
title | Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives |
title_full | Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives |
title_fullStr | Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives |
title_full_unstemmed | Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives |
title_short | Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives |
title_sort | complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830136/ https://www.ncbi.nlm.nih.gov/pubmed/35139817 http://dx.doi.org/10.1186/s12864-022-08336-8 |
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