Abstract Detail

Comparative Genomics/Transcriptomics

Bailey, C. Donovan [1], Strickler, Susan [2], Ringelberg, Jens J. [3], Koenen, Erik J.M. [3], Liston, Aaron [4], Nagaswara-Rao, Madhugiri [5], Abair, Alexander [6], Hughes, Colin E [7].

A Reference Quality Genome Assembly and Investigation of Genome Duplication in the Mimosoid Legume Leucaena trichandra.

Continued development of next generation sequencing technologies has led to massive advances in the quality and availability of complex angiosperm reference genome assemblies for comparative genomic research. A number of these genomes represent the ecologically and economically important Leguminosae, but these largely focus on agriculturally important crops and the two model legumes in subfamily Papilionoideae (e.g., Glycine, Phaseolus, Vigna, Lotus, Medicago,). Genome assemblies for the other five legume subfamilies are currently of poor quality or lacking, limiting our understanding of the overall diversity of legume genomic variation, origins of symbiotic nitrogen fixation, or elements of human-plant co-evolution. One such lineage is the genus Leucaena, a member of the mimosoid clade within subfamily Caesalpinioideae. The genus Leucaena as a whole is paleopolyploid and includes 19 ‘diploid’ and 5 neoallotetraploid species, found in the seasonally dry warm temperate to tropical regions of Central and South America, with historical importance as minor food crops, a complex history of spontaneous interspecific hybridization, and modern uses in multipurpose tropical agriculture. Here we present a genome assembly for L. trichandra, a putative diploid taxon whose genome has been implicated in the origins of four of the five allopolyloid species of Leucaena. Using a combination of long-read PacBio data for contig development, Hi-C data for scaffolding, and Illumina libraries for polishing, we present a high quality assembly that comprises 28 pseudochromosomes and an estimated BUSCO protein coding completeness of 97%. The genome assembly encompasses features consistent with a whole genome duplication event predating the diversification of extant “diploid” Leucaena. Using this genome and transcriptome data from all “diploid” species of Leucaena, alongside existing legume genomic and transcriptomic data, we investigate the phylogenetic placement of the WGD that predates diversification of Leucaena as well as the downstream fates of duplicate gene copies.

1 - New Mexico State University, Biology, Rm 120 Foster Hall (Stores), Dept Of Biology - New Mexico State University, Las Cruces, NM, 88003, United States
2 - Boyce Thompson Institute For Plant Research , 533 Tower Road, Ithaca, NY, 14853, United States
3 - University of Zurich, Department of Systematic and Evolutionary Botany, Zollikerstrasse 107, Zurich, CH‐8008, Switzerland
4 - Oregon State University, Department Of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331, United States
5 - USDA, Plant Genetics, 13601 Old Cutler Rd, Miami, FL, 33158, USA
6 - University Of Florida, Department Of Biology, 1659 Museum Rd, Gainesville, FL, 32611, United States
7 - University Of Zurich, Institute Of Systematic And Evolutionary Botany, Zollikerstrasse 107, Zürich, ZH, 8008 Zürich, Switzerland

Keywords:
genomics
Comparative genomics
PacBio
Genome Duplication.

Presentation Type: Oral Paper
Session: CGT3, Comparative Genomics/Transcriptomics III
Location: /
Date: Tuesday, July 20th, 2021
Time: 3:45 PM(EDT)
Number: CGT3004
Abstract ID:516
Candidate for Awards:None