Medicago truncatula aka barrelclover is an annual legume native to the Mediterranean region. It is a low-growing, clover-like plant 10–60 centimetres (3.9–23.6 in) tall with trifoliate leaves. Each leaflet is rounded, 1–2 centimetres (0.39–0.79 in) long, often with a dark spot in the center. The flowers are yellow, produced singly or in a small inflorescence of two to five together; the fruit is a small, spiny pod.
This species is studied as a model organism for legumes, a plant family that includes soybeans, peanuts, peas and alfalfa, because it has a small diploid genome, is self-fertile, has a rapid generation time and prolific seed production. As such, extensive genomic studies of the species have been undertaken, and a genome assembly for the species has been available to the community thanks to the efforts of the Medicago truncatula Consortium (see Young et al., 2017; Tang et al., 2014).
Unfortunately, the reference genotype (Jemalong A17) originally selected for the chromosome-length genome sequencing and assembly proved to be recalcitrant to transformation. M. truncatula R108 accession is more attractive for genetic studies due to its high transformation efficiency and functional genomic resources, but has been lacking a chromosome-length genome assembly.
To address this we performed in situ Hi-C (~30×) to anchor, order, orient scaffolds, and correct misjoins in contigs from a draft genome assembly for the R108 barrelclover from (Moll et al., 2017) resulting in a chromosome-length genome assembly. The new assembly allowed us to accurately annotate the chromosome 4/8 translocation between the R105 and A17 accessions as well as map the Tnt1 retrotransposon insertions creating a resource for downstream insertional mutagenesis studies. Read more about this in our research article “Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly” now available open access in IJMS, Special Issue - Functional Genomics for Plant Breeding 2.0.
We gratefully acknowledge the frozen leaf sample provided by Scott Schaeffer at the Nakata Lab (USDA, ARS). The Hi-C work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.
The following people contributed to the Hi-C chromosome-length upgrade of the project: Christopher Lui, Melanie Pham, Olga Dudchenko, Erez Aiden & Parwinder Kaur.
Blog by: Parwinder Kaur