Abstract Detail

Applications of Plant Genomics

Finch, Kristen [1], Cronn, Richard [2].

Using ex-situ collections to disentangle a Cedrela - Toona sandwich.

Herbaria and botanical gardens accumulate comprehensive sources of genetic material from broad taxonomic and geographic ranges that would be logistically impossible to replicate on a single botanical expedition. This is especially true for taxa that span large geographic areas, such as multiple countries, continents, or hemispheres. Over 10 non-sequential days, we collected leaf tissue from 192 Cedrela (Meliaceae) specimens ranging from Nicaragua to northern Argentina by visiting the Missouri Botanical Garden Herbarium (MO). Using the ex-situ tropical collection at the New York Botanical Garden (NYBG), we obtained fresh RNA and DNA from a Cedrela odorata specimen that originated in Oaxaca, Mexico, and were able to assemble a reference transcriptome and chloroplast genome for this species. Using only these ex-situ collections, we developed hybridization capture probes that allowed us to capture, sequence, and assemble 10,000 low-copy genes, as well as sequence and assemble full chloroplast genomes from these 192 specimens. Despite our success, our study did not escape the pitfalls associated with ex-situ collections. For example, we identified 23 specimens that may be misidentified, including the NYBG specimen used for our reference transcriptome and chloroplast genome. To solve these classification mysteries, we returned to MO and re-collected leaf tissue from the remaining Central American Cedrela odorata and related Cedrela species. Targeted chloroplast genome sequencing (matK; trnH-psbA) allowed us to accurately classify our reference specimen, as well as clarify the apparently paraphyletic relationship between Cedrela and its Old-World sister genus Toona. The high-quality Cedrela reference specimens from MO provided a valuable reference dataset for molecular identification of suspect taxa, and also provide genomic resources that are transferrable across the genus Cedrela and even Swietenia mahagoni (L.) Jacq.. Together, these resources are being used to develop genotyping arrays that can be used to identify the geographic origin of Cedrela odorata specimens, and the taxonomic identity of Cedrela species-level. These arrays will be valuable for evolutionary studies focused on Cedrela, and for the regulation of illegal logging of this historically over-exploited plant group.

1 - Oregon State University, Botany And Plant Pathology, Cordley Hall 2082; 2701 SW Campus Way, Corvallis, OR, 97331, United States
2 - 3200 SW Jefferson Way, Corvallis, OR, 97330, United States

Keywords:
Cedrela
collections
herbarium specimens
De novo Transcriptome
botanical garden
Chloroplast genome
Genomics
Targeted Sequence Capture
Swientia mahagoni
Toona
Cedrela odorata
genotyping array.

Presentation Type: Colloquium Presentations
Session: C13, Applications of Plant Genomics
Location: 104/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 4:00 PM
Number: C13009
Abstract ID:743
Candidate for Awards:Margaret Menzel Award