Abstract Detail

Comparative Genomics/Transcriptomics

Landis, Jacob [1], Valderrama, Eugenio [2], Grunder, Nikolaus [3], Skinner, David [4], Pinilla Vargas, Maria [5], Almeida, Ana [3], Specht, Chelsea [6].

Using de novo assemblies to identify genomic signatures of evolution between insect and hummingbird pollination in Costus (Costaceae).

The angiosperm genus Costus L., also known as the spiral gingers, is comprised of roughly 80 species with a widespread distribution through tropical and subtropical regions of Africa and the Americas and accounts for much of the species diversity within the family Costaceae Nakai. Throughout the genus there is a diversity of floral forms associated with pollinator attraction and pollination efficiency. Phylogenetic analyses have identified multiple transitions from insect to bird pollination across the genus, associated with strikingly consistent shifts in floral morphology. Using a combination of sequencing approaches, we have generated 80X short-read data from Illumina and around 20x long-read coverage from Oxford Nanopore for 10 species pairs for de novo genome assembly. Even though we have not achieved chromosome level assemblies, we are recovering at least 80% of the Embryophyta BUSCO genes, giving confidence in comparative analyses. Genome annotation was carried out with Maker using a combination of Illumina short-reads and Oxford Nanopore long-read RNASeq data generated from leaf and floral tissue. Downstream comparative genomic analyses allowed for identification of genomic regions associated with shifts in pollinator and repeated transitions potentially involving the same locus (or loci) with differing regulatory constraints, as well as comparisons of estimated genome size using kmer counting.

1 - Cornell University, School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14850, USA
2 - Cornell University, Plant Biology, CALS, 510 Mann Library, Ithaca, NY, 14853, United States
3 - Cal State East Bay
4 - Unaffiliated
5 - Cornell University, Ithaca, NY, 14853, United States
6 - Cornell University, Section of Plant Biology & the L.H. Bailey Hortorium, 502 Mann Library, Ithaca, NY, 14853, United States

Keywords:
Costus L.
nanopore
pollinator shifts
Genome Assembly.

Presentation Type: Oral Paper
Session: CGT1, Comparative Genomics/Transcriptomics I
Location: /
Date: Tuesday, July 20th, 2021
Time: 11:15 AM(EDT)
Number: CGT1006
Abstract ID:739
Candidate for Awards:Margaret Menzel Award