An improved genome release (version Mt4.0) for the model legume Medicago truncatula

Area of Science:

• Plant Genomics
• Legume Biology
• Symbiosis Research

Background:

• Medicago truncatula is a key model organism for studying nitrogen fixation, symbiosis, and legume genomics.
• Previous genome assembly (Mt3.5) was based on a BAC tiling path, with initial analysis published in 2011.

Purpose of the Study:

• To describe an improved and refined version of the Medicago truncatula genome assembly, designated Mt4.0.
• To enhance the accuracy and completeness of the M. truncatula genome sequence and gene annotation.

Main Methods:

• Utilized de novo whole genome shotgun assembly with Illumina and 454 reads via ALLPATHS-LG.
• Anchored scaffolds to pseudomolecules using optical map and genotyping-by-sequencing (GBS) map alignments.
• Re-annotated the genome using a pipeline integrating EST, RNA-seq, protein, and gene prediction evidence.

Main Results:

• The Mt4.0 assembly encompasses ~360 Mb of sequences, a substantial improvement over the ~250 Mb in Mt3.5.
• Incorporated most previously unanchored sequences and genes from Mt3.5 into Mt4.0 pseudomolecules.
• Annotated 50,894 genes in Mt4.0, with significant overlap and improvements over Mt3.5 gene loci.

Conclusions:

• The Mt4.0 genome assembly and associated resources are publicly available via the JCVI Medicago web site.
• The assembly and annotation data have been deposited in GenBank (BioProject: PRJNA10791).
• Mt4.0 provides a superior reference for legume biology and comparative genomics research.