Abstract Detail

Comparative Genomics/Transcriptomics

Catalan, Pilar [1], Sancho, Ruben [2], Inda, Luis Angel [3], Diaz-Perez, Antonio [3], Des Marais, David [5], Gordon, Sean [6], Vogel, John [6], Contreras-Moreira, Bruno [7].

Subgenome-detection algorithms and cross-bracing dating approaches reveal the ancestry of known and ‘ghost’ homeologous subgenomes in grass Brachypodium allopolyploids.

Unravelling the evolution of plant allopolyploids is a challenge when their diploid progenitors are extinct or unknown and their genome sequence is incomplete. Subgenome identification methods could not adequately retrieve all the diploid homeologous genomes present in the allopolyploids if the searching algorithms do not take into account the potential existence of unknown progenitors. We address this challenge in the widely dysploid grass model genus Brachypodium by using a transcriptome-based phylogeny and newly designed subgenome detection algorithms. We have benchmarked the subgenome detection algorithms with Triticum genomic data. We infer the identities of the subgenomes and the hybridization events that created six allopolyploid Brachypodium species, all but one of which contain unobserved diploid homeologous genomes. We have analysed cytogenetic and RNA-seq data from 11 diploid and polyploid Brachypodium species (12 accessions) representing two thirds of the recognized taxa in the genus, which cover all the main diversification and hybridization events across its phylogeny. We used a novel phylogenomic strategy to uncover the homeologous subgenomes of the allopolyploids. Our multigene-based phylogenetic approach combines our nearest diploid species node and subgenome assignation algorithms, together with informed cytogenetic data, and infers the identity and evolutionary history of all the diploid subgenomes present in the studied allopolyploids. We have treated the subgenomes of allopolyploids as species and have employed cross-bracing methods to estimate the age of the hybridization events involved in the origin of each allopolyploid. Our approach could be used to identify “ghost” subgenomes in other allopolyploid plants of unknown diploid and lower-ploidy ancestors.

1 - Escuela Politecnica Ctra. Cuarte Km 1, Huesca, HU, 22071, Spain
2 - Escuela Politecnica , Ctra. Cuarte Km 1, Huesca, HU, 22071, Spain
3 - Escuela Politecnica, Ctra. Cuarte Km 1, Huesca, HU, 22071, Spain
4 - Escuela Politecnica, Ctra. Cuarte Km 1, Huesca, HU, 22071, Spain
5 - Massachusetts Institute of Technology (MIT), Department of Civil and Environmental Engineering, Cambridge, MA, USA
6 - DOE Joint Genome Institute, Walnut Creek, CA, USA
7 - Estación Experimental de Aula Dei-CSIC, Department of Genetics and Plant Breeding, Zaragoza, Z, Spain

 core genes
homeologous subgenomes

Presentation Type: Oral Paper
Session: CG2, Functional & Comparative Genetics/Genomics II
Location: Virtual/Virtual
Date: Wednesday, July 29th, 2020
Time: 3:15 PM
Number: CG2002
Abstract ID:250
Candidate for Awards:Margaret Menzel Award

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