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Abstract Detail


Bogler, David [1], Worth, Nia [2].

Exploring Agave Phylogenomics with Nanopore MinION Technology.

Agave is a genus of 200 species in dry habitats of Mexico, Southwestern U.S., and Caribbean, classified in Asparagaceae, subfamily Agavoideae. Very little is known about subgeneric relationships in Agave due to low sequence variation. The objective of our study was to assess the current status of Agave phylogenomics using a combination of karyotype information and sequences downloaded from GenBank. In addition we sequenced the entire chloroplast genome of Agave arizonica using the Oxford Nanopore MinION sequencer to assess its potential for future studies using whole chloroplast genomes. The MinION is a “Third Generation” sequencer that plugs into a laptop. Large fragments of DNA are passed through pores embedded in a membrane, with changes in electrical current identifying the bases. The MinION is relatively inexpensive and holds great promise for generation large amounts of sequence data. Bud material from living Agavoideae was collected and chromosomes imaged using the acetocarmine squash technique. The literature was reviewed to assemble chromosome number and ploidy level for Agave and Agavoideae. Karyotypes are distinctively bimodal in this group, commonly n=30 with 25 small chromosomes and 5 large. However, some basal members have n=15 and possibly represent the oldest lineages. Higher polyploidy occurs in some species of Agave. The downloaded sequences (rbcL, matK, trnL-F spacer, trnL intron, and ITS2) from 25 Agavoideae were aligned, the matrices concatenated into a single matrix with 2,700 characters, and analyzed using MrBayes. The resulting tree was well-resolved, and compared favorably with recent whole chloroplast genome studies, although resolution within Agave is weak. The n=15 taxa of Agavoideae are basal and this suggests the group originated in the New World. The MinION experiment resulted in 1,103 cpDNA sequence fragments that were aligned to a reference chloroplast genome of Agave americana from GenBank using Geneious software. The average coverage was 4.9 and average read length was about 800 bp. With more careful purification and quantification of DNA extracts we hope to employ barcodes to examine more species in a single MinION run.

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1 - Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO, 63110, United States
2 - Harris-Stowe State University, Math and Natural Science, 3026 Laclede Ave., St. Louis, MO, 63103, USA

none specified

Presentation Type: Poster
Session: P, Systematics Posters
Location: Arizona Ballroom/Starr Pass
Date: Monday, July 29th, 2019
Time: 5:30 PM This poster will be presented at 6:15 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PSY024
Abstract ID:1018
Candidate for Awards:None

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