Abstract Detail



Phylogenomics

Soto Gomez, Marybel [1], Viruel, Juan  [2], Kantar , Michael [3], Wilkin, Paul [4], Graham, Sean [5].

A phylogenomics pipeline for identifying crop wild relatives: an example from the Dioscorea yams, a major pantropical crop.

The Dioscorea yams are one of the three most important tropical tuber crops along with cassava and sweet potato. Multiple species in the genus have been brought into cultivation for starch-rich annual tubers that provide a major source of nutrition and income to millions of subsistence farmers in the tropics. Yams with perennial tubers and rhizomes have also been used for pharmaceutically useful compounds, such as diosgenin. Although progress has been made in understanding species-level relationships in Dioscorea, multiple uncertainties persist, including the precise identity of crop wild relatives (CWRs) of major yam cultigens. A phylogenetic framework for the genus would be useful for identifying CWRs that may represent genetically similar pools for germplasm selection and crop improvement. We are addressing this knowledge gap by using targeted enrichment of nuclear genes from wild-collected species, using RNA probes to retrieve 260 single- to low-copy nuclear genes from ~400 species of Dioscorea represented largely by herbarium material. This sampling strategy spans the taxonomic diversity of the genus, and includes all major yam crop species and putative CWRs. We present results from an initial 39-taxon phylogenomic analysis that includes representatives from the major Dioscorea clades. Using target enrichment methods we recovered target sequences for 151-259 single- to low-copy nuclear genes from 25 taxa, adding these to transcriptome-derived data from an additional 14 taxa for the same nuclear genes. After identifying and removing genes with potential duplicates, we applied coalescent-based tree inference methods using 252 nuclear genes. Our results strengthen our understanding of relationships among the major Dioscorea clades, and resolve most interspecific relationships with strong support, including those between a cultigen (D. alata), a previously proposed CWRs (D. nummularia) and an additional species that had not been identified as a CWR.


1 - University of British Columbia, Botany, 3200-6270 University Blvd, Vancouver, Canada, V6T 1Z4, Canada
2 - Royal Botanic Gardens, Kew, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
3 - University of Hawai'i, Manoa, Tropical Plant and Soil Sciences, 3190 Maile Way, Honolulu, HI, 96822, USA
4 - Royal Botanic Gardens, Kew, Natural Capital and Plant Health, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
5 - University of British Columbia, Botany, 3200 Biological Sciences Build, 6270 UNIVERSITY BLVD, Vancouver, Canada, V6T 1Z4, Canada

Keywords:
Phylogenomics methods
Nuclear monocot phylogenomics
Hyb-Seq
Dioscoreaceae
Dioscoreales
low-copy nuclear loci.

Presentation Type: Oral Paper
Session: 36, Phylogenomics III
Location: 107/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 8:30 AM
Number: 36003
Abstract ID:744
Candidate for Awards:None


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