Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies

TL;DR

This paper presents a detailed chromosome-scale genome assembly for Malcolmia littorea, a plant adapted to coastal environments, using advanced sequencing and genotyping methods.

Contribution

The study introduces a novel single-pollen genotyping method to anchor genome sequences to chromosomes in M. littorea.

Findings

A chromosome-scale genome assembly of 215 Mb with 30,266 predicted genes was created for M. littorea.

The genome is twice the size of Arabidopsis thaliana's genome, suggesting a whole-genome duplication followed by subfunctionalization or neofunctionalization.

Abstract

Malcolmia littorea, a member of the family Brassicaceae, is adapted to coastal and sandy environments and has become a model in studies of reproductive barriers. However, genomic resources for the species are limited. Here, with the aim of understanding the molecular mechanisms underlying key traits in M. littorea, we present a de novo genome assembly consisting of 10 chromosome-scale sequences. We employed a high-fidelity long-read sequencing technology for genome assembly. To anchor the sequences to chromosomes, we developed a single-pollen genotyping method to construct a genetic linkage map based on SNPs derived from transcriptomes of pollen grains, possessing recombinant haploid genomes. We built a genome assembly consisting of 10 chromosome-scale sequences (215 Mb in total) for M. littorea containing 30,266 predicted genes. A comparative genome analysis and gene prediction indicated that the genome of M. littorea is double the size of the Arabidopsis thaliana genome, consistent with a whole-genome duplication followed by gene subfunctionalization and/or neofunctionalization in M. littorea. This study provides a basis for research on M. littorea, an understudied species with ecological and evolutionary significance.

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