Abstract Detail

Comparative Genomics/Transcriptomics

DaCosta, Jeffrey [1], Yant, Levi [2], Potter, Daniel [3], Mathews, Sarah [4].

Comparative genomics of a species radiation: sequencing the apple tribe.

Understanding the evolution of species radiations and how genome evolution progresses in this context remains a central problem in biology. An intriguing and important radiation within Rosaceae produced a clade of about 750 woody species distributed in 35 genera with a base chromosome number of x = 17 (tribe Maleae) that includes the apple, pear, and quince genera. The sister group of this clade is the genus Gillenia, which has just two species, both herbaceous perennials with a base chromosome number of x = 9. The Maleae are particularly attractive for the study of genome evolution in the context of a species radiation because of their generally small genome sizes and their origin following a single whole genome duplication (WGD) that postdates their divergence from Gillenia. Early diverging Maleae are similar to Gillenia in having dry fruits and few species. But after the evolution of the pome, they diversified into 32 genera, sorting into lineages with distinctive phenotypic, life history, and ecological traits, including lineages in which repeated hybridization and polyploidy events have contributed to their species-richness. We have produced draft genome assemblies for representative Maleae and outgroups in order to explore the potential impacts of WGD and post-WGD genome evolution on diversification of the Maleae. Specifically, we are reconstructing patterns of lineage-specific gene loss and retention, characterising the expansion and contraction of gene families, and testing for evidence of variable selective pressures. Preliminary results so far suggest that for genes that were single copy before WGD and were subsequently retained as no more than two copies (13,499), about half have reverted to single copy in Maleae. Of the genes that are retained as two-copy, about half are retained in both dry- and pome-fruited taxa and the other half in pome-fruited Maleae only, while a very small proportion of the two-copy genes are retained in dry-fruited taxa only. From these data, we will reconstruct patterns of loss and discuss the results in the context of the potential contribution of reciprocal gene loss to reproductive isolation. We also will discuss findings on rates of gene loss and gain across the Maleae phylogeny, and on specific gene families characterised by expansions and contractions in copy number.

1 - Boston College, Biology Department, Chestnut Hill, MA, 02467, USA
2 - John Innes Centre, Norwich, NR4 7UH, UK
3 - University Of California, Plant Sciences Mail Stop 2, 1 Shields Avenue, Davis, CA, 95616.0, United States
4 - CSIRO National Research Collections Australia, Australian National Herbarium, Clunies Ross Street, GPO 1700, Canberra, ACT, 2601, Australia

Keywords:
Maleae
Rosaceae
Comparative Genomics
whole genome duplication.

Presentation Type: Oral Paper
Session: 25, Comparative Genomics and Transcriptomics II
Location: 102/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 4:30 PM
Number: 25014
Abstract ID:688
Candidate for Awards:Margaret Menzel Award