A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae
Premise The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2020-10-01
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| Series: | Applications in Plant Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/aps3.11394 |
| _version_ | 1817984811558502400 |
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| author | Brian J. Sanderson Stephen P. DiFazio Quentin C. B. Cronk Tao Ma Matthew S. Olson |
| author_facet | Brian J. Sanderson Stephen P. DiFazio Quentin C. B. Cronk Tao Ma Matthew S. Olson |
| author_sort | Brian J. Sanderson |
| collection | DOAJ |
| description | Premise The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus. Methods We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300–1200 bp of exonic regions of 972 genes. Results We recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci. Conclusions Our sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies. |
| first_indexed | 2024-04-13T23:50:08Z |
| format | Article |
| id | doaj.art-ab5a4efcfccf46f690120a75880de7ae |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-04-13T23:50:08Z |
| publishDate | 2020-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-ab5a4efcfccf46f690120a75880de7ae2022-12-22T02:24:08ZengWileyApplications in Plant Sciences2168-04502020-10-01810n/an/a10.1002/aps3.11394A targeted sequence capture array for phylogenetics and population genomics in the SalicaceaeBrian J. Sanderson0Stephen P. DiFazio1Quentin C. B. Cronk2Tao Ma3Matthew S. Olson4Department of Biological Sciences Texas Tech University Lubbock Texas79409‐3131USADepartment of Biology West Virginia University Morgantown West Virginia26506USADepartment of Botany University of British Columbia Vancouver British ColumbiaV6T 1Z4CanadaKey Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu610065People’s Republic of ChinaDepartment of Biological Sciences Texas Tech University Lubbock Texas79409‐3131USAPremise The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus. Methods We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300–1200 bp of exonic regions of 972 genes. Results We recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci. Conclusions Our sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.https://doi.org/10.1002/aps3.11394phylogeneticsPopulusSalicaceaeSalixtargeted sequence capture |
| spellingShingle | Brian J. Sanderson Stephen P. DiFazio Quentin C. B. Cronk Tao Ma Matthew S. Olson A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae Applications in Plant Sciences phylogenetics Populus Salicaceae Salix targeted sequence capture |
| title | A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae |
| title_full | A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae |
| title_fullStr | A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae |
| title_full_unstemmed | A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae |
| title_short | A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae |
| title_sort | targeted sequence capture array for phylogenetics and population genomics in the salicaceae |
| topic | phylogenetics Populus Salicaceae Salix targeted sequence capture |
| url | https://doi.org/10.1002/aps3.11394 |
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