Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era
Abstract Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2020-02-01
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| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.5984 |
| _version_ | 1818670934669656064 |
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| author | Shing Hei Zhan Chun‐Chi Shih Shao‐Lun Liu |
| author_facet | Shing Hei Zhan Chun‐Chi Shih Shao‐Lun Liu |
| author_sort | Shing Hei Zhan |
| collection | DOAJ |
| description | Abstract Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof‐of‐concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence‐derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae. |
| first_indexed | 2024-12-17T07:16:00Z |
| format | Article |
| id | doaj.art-470fee0acaf14e50a2a4de2c59857f4a |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-12-17T07:16:00Z |
| publishDate | 2020-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-470fee0acaf14e50a2a4de2c59857f4a2022-12-21T21:58:54ZengWileyEcology and Evolution2045-77582020-02-011031299131010.1002/ece3.5984Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic eraShing Hei Zhan0Chun‐Chi Shih1Shao‐Lun Liu2Department of Zoology & Biodiversity Research Centre the University of British Columbia Vancouver BC CanadaDepartment of Life Science & Center for Ecology and Environment Tunghai University Taichung TaiwanDepartment of Life Science & Center for Ecology and Environment Tunghai University Taichung TaiwanAbstract Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof‐of‐concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence‐derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.https://doi.org/10.1002/ece3.5984environmental DNA metabarcodingphylogenetic inferencephylogenomicsplastid genomesrbcLrpoC1 |
| spellingShingle | Shing Hei Zhan Chun‐Chi Shih Shao‐Lun Liu Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era Ecology and Evolution environmental DNA metabarcoding phylogenetic inference phylogenomics plastid genomes rbcL rpoC1 |
| title | Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era |
| title_full | Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era |
| title_fullStr | Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era |
| title_full_unstemmed | Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era |
| title_short | Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era |
| title_sort | reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era |
| topic | environmental DNA metabarcoding phylogenetic inference phylogenomics plastid genomes rbcL rpoC1 |
| url | https://doi.org/10.1002/ece3.5984 |
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