Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae)
Premise of the study: The genus <i>Ficus</i> (fig trees) comprises ca. 750 species of trees, vines, and stranglers found in tropical forests throughout the world. Fig trees are keystone species in many tropical forests, and their relationship with host-specific wasp pollinators has recei...
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| Format: | Article |
| Language: | English |
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Wiley
2013-10-01
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| Series: | Applications in Plant Sciences |
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| Online Access: | http://www.bioone.org/doi/full/10.3732/apps.1300037 |
| _version_ | 1818600355092496384 |
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| author | Xiaohong Yao Chenhong Li Christopher W. Dick |
| author_facet | Xiaohong Yao Chenhong Li Christopher W. Dick |
| author_sort | Xiaohong Yao |
| collection | DOAJ |
| description | Premise of the study: The genus <i>Ficus</i> (fig trees) comprises ca. 750 species of trees, vines, and stranglers found in tropical forests throughout the world. Fig trees are keystone species in many tropical forests, and their relationship with host-specific wasp pollinators has received much attention, although many questions remain unresolved regarding the levels of host specificity, cospeciation, and the role of hybridization in fig and wasp speciation. We developed exon-primed intron-crossing (EPIC) markers to obtain phylogenetic resolution needed to address these questions.
Methods and Results: Expressed sequence tags (ESTs) from F. elastica were compared to <i>Arabidopsis</i> and <i>Populus</i> genomes to locate introns and to design primers in flanking exons. Primer pairs for 80 EPIC markers were tested in samples from divergent clades within <i>Ficus</i> and the outgroup <i>Poulsenia</i> (Moraceae).
Conclusions: Thirty-one EPIC markers were successfully sequenced across <i>Ficus</i>, and 29 of the markers also amplified in <i>Poulsenia</i>, indicating broad transferability within Moraceae. All of the EPIC markers were polymorphic and showed levels of polymorphism similar to that of the widely used internal transcribed spacer (ITS). |
| first_indexed | 2024-12-16T12:34:10Z |
| format | Article |
| id | doaj.art-3baa45de043740089333f178d8a8ceee |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-12-16T12:34:10Z |
| publishDate | 2013-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-3baa45de043740089333f178d8a8ceee2022-12-21T22:31:37ZengWileyApplications in Plant Sciences2168-04502013-10-01110130003710.3732/apps.1300037Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae)Xiaohong Yao0Chenhong Li1Christopher W. Dick2Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, People's Republic of China; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-1048 USAKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of ChinaDepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-1048 USA; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa, Ancón, Republic of PanamaPremise of the study: The genus <i>Ficus</i> (fig trees) comprises ca. 750 species of trees, vines, and stranglers found in tropical forests throughout the world. Fig trees are keystone species in many tropical forests, and their relationship with host-specific wasp pollinators has received much attention, although many questions remain unresolved regarding the levels of host specificity, cospeciation, and the role of hybridization in fig and wasp speciation. We developed exon-primed intron-crossing (EPIC) markers to obtain phylogenetic resolution needed to address these questions. Methods and Results: Expressed sequence tags (ESTs) from F. elastica were compared to <i>Arabidopsis</i> and <i>Populus</i> genomes to locate introns and to design primers in flanking exons. Primer pairs for 80 EPIC markers were tested in samples from divergent clades within <i>Ficus</i> and the outgroup <i>Poulsenia</i> (Moraceae). Conclusions: Thirty-one EPIC markers were successfully sequenced across <i>Ficus</i>, and 29 of the markers also amplified in <i>Poulsenia</i>, indicating broad transferability within Moraceae. All of the EPIC markers were polymorphic and showed levels of polymorphism similar to that of the widely used internal transcribed spacer (ITS).http://www.bioone.org/doi/full/10.3732/apps.1300037exonsFicusMoraceaenuclear DNA markersphylogenytranscriptome |
| spellingShingle | Xiaohong Yao Chenhong Li Christopher W. Dick Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae) Applications in Plant Sciences exons Ficus Moraceae nuclear DNA markers phylogeny transcriptome |
| title | Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae) |
| title_full | Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae) |
| title_fullStr | Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae) |
| title_full_unstemmed | Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae) |
| title_short | Exon-Primed Intron-Crossing (EPIC) Markers for Evolutionary Studies of <i>Ficus</i> and Other Taxa in the Fig Family (Moraceae) |
| title_sort | exon primed intron crossing epic markers for evolutionary studies of i ficus i and other taxa in the fig family moraceae |
| topic | exons Ficus Moraceae nuclear DNA markers phylogeny transcriptome |
| url | http://www.bioone.org/doi/full/10.3732/apps.1300037 |
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