De novo assembly of the whole genome of Moth bean (Vigna aconitifolia), an underutilized Vigna species of India

Suranjika, S.; Pradhan, S.; Kalia, R. K.; Dey, N.

doi:10.1101/2023.05.18.540937

Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.05.18.540937

De novo assembly of the whole genome of Moth bean (Vigna aconitifolia), an underutilized Vigna species of India

Suranjika, S.·Pradhan, S.·Kalia, R. K.·Dey, N.

View original source ↗Export metadata ↓

Abstract

As a fast-growing legume species, moth bean (Vigna aconitifolia) has a unique habit of sustaining in conditions of higher temperatures and drought. This grain legume is also valued for it seeds which have one of the highest contents of proteins amongst all grain legumes. This plant can be a rich source of genomic resources, which can be applied to improve abiotic stress response in allied grain legumes and also help understand the biological processes governing their overall development. Here we generate a de novo genome assembly of Vigna aconitifolia using PacBio High-Fidelity reads and Hi-C sequencing data, with a total size of 409 Mb and contig N50 of more than 30Mb. We also annotated the genome for repeat sequences, found that the moth bean genome comprises of about 54% of repetitive sequences, and predicted 36950 protein-coding genes. Using the available RNA-Seq data for moth bean, we have developed a differential expression profile for various tissues of moth bean using the whole genome as a reference and identified simple sequence repeats that could be developed into viable molecular markers. This nascent study will provide insight into the identification of agronomically important genes and accelerate the genetic improvement of moth bean as well as other legume crops.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Suranjika, S., Pradhan, S., Kalia, R. K., Dey, N.. 2023-05-19. De novo assembly of the whole genome of Moth bean (Vigna aconitifolia), an underutilized Vigna species of India. https://doi.org/10.1101/2023.05.18.540937

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

MicroDUET: a dual-headed genomic foundation model for pathogen surveillance

Pathogen genomic surveillance works from raw reads, assembled genomes and alignments, representations that are slow and costly to compare at scale. Compact embeddings from genomic language models offer an alternative, but surveillance requires resolving both evolutionary ancestry (phylogeny) and phenotypic capability (function) - which need not co-vary. Here we present MicroDUET, which adapts a 26.6-million-parameter ProkBERT backbone with two 3.5-million-parameter adapter heads: a phylogeny head trained contrastively on genome windows from the same microbes, and a function head trained to identify genes across taxa. On held-out retrieval benchmarks, the phylogeny head returned the correct species for 80.3% and 66.6% of cellular and viral queries, and the function head the correct gene family for 97.3% and 97.2%, reaching 74.4% accuracy on an independent antimicrobial resistance-class benchmark. Across all three benchmarks MicroDUET outranked 17 other genomic encoders. Without training on lineage, clade or drug-susceptibility tasks, MicroDUET identified Mycobacterium tuberculosis and mpox virus lineages and clades (0.965, 0.975 accuracy), discriminated rifampicin resistance without lineage adjustment (AUROC 0.985), and retrospectively identified an emerging mpox lineage as anomalous (AUROC 0.974). MicroDUET operates 10^3 - 10^4 times faster than single-threaded sequence-based alignments. MicroDUET therefore provides a compact, reusable representation for scalable pathogen surveillance and sequence triage.

genomics↗

bioRxiv2026

A chromosome-level genome assembly of northern dragonhead, Dracocephalum ruyschiana L., 1753

We present a chromosome-level genome assembly for the vascular plant northern dragonhead, Dracocephalum ruyschiana. The assembly comprises two pseudo-haplotypes, hap1 and hap2, of 661 Mb and 681 Mb, with 93.6% and 92.5%, respectively, scaffolded into seven chromosomes each - in line with the known karyotype. Assembly quality was high, with conserved single-copy ortholog completeness scores of 97.9% and 97.8%, combined k-mer completeness of 98.1%, and 38,141 and 38,617 annotated protein-coding genes for hap1 and hap2, respectively. This assembly provides a high-quality genomic resource for future research and conservation of northern dragonhead, as well as the endangered northern dragonhead sap beetle, which depends on the plant for reproduction and whose genome assembly is described in a complementary genome note.

genomics↗

bioRxiv2026

Elucidating Bat SuperImmunity: Insights from the Bent-Wing Bat Genome Assembly and Multi-Omics Analysis

Bats have evolved a range of unique adaptations, including powered flight, echolocation, and exceptional longevity. They have also attracted considerable scientific attention, particularly since the COVID-19 pandemic, due to their association with a broad diversity of viruses and their potential role in zoonotic transmission and emerging infectious diseases. Despite hosting numerous viruses, bats often exhibit limited clinical manifestations of infection, suggesting the evolution of distinctive mechanisms of immune regulation and tolerance. Understanding the molecular basis of these mechanisms has become a major focus of current research, with genome-wide analyses providing important insights into the genetic adaptations underlying bat immunity. Nevertheless, the regulatory complexity of bat genomes, particularly the contribution of non-coding RNAs and post-transcriptional RNA editing, remains comparatively underexplored. Here, we present an integrated multi-omic framework for the common bent-wing bat (Miniopterus schreibersii), combining a contiguous chromosome-scale genome assembly with multi-tissue transcriptomic profiling, long non-coding RNA (lncRNA) identification and synteny analysis, endogenous viral elements (EVE) mapping, and same-individual RNA editomic analyses. This study provides a comprehensive resource for investigating genome organization, transcriptional regulation, evolutionary relationships, and post-transcriptional modifications in this species. In particular, it offers an opportunity to explore the potential contribution of non-coding regulatory elements and RNA editing to the molecular mechanisms underlying viral interactions and immune regulation in bats. Collectively, these resources provide a valuable foundation for advancing our understanding of bat genome evolution and the regulatory mechanisms potentially associated with their distinctive responses to viral infections.

genomics↗