-
A de novo chromosome-scale assembly of the Lablab purpureus genome
- Back
Document Title
A de novo chromosome-scale assembly of the Lablab purpureus genome
Author
Pootakham W. Somta P. Kongkachana W. Naktang C. Sonthirod C. U-Thoomporn S. Yoocha T. Phadphon P. Tangphatsornruang S.
Affiliations
National Center for Genetic Engineering and Biotechnology BIOTEC) National Science and Technology Development Agency (NSTDA Pathum Thani Thailand; Department of Agronomy Faculty of Agriculture at Kamphaeng Saen Kasetsart University Nakhon Pathom Thailand
Type
Article
Source Title
Frontiers in Plant Science
ISSN
1664462X
Year
2024
Volume
15
Open Access
All Open Access Gold
Publisher
Frontiers Media SA
DOI
10.3389/fpls.2024.1347744
Abstract
Introduction: Lablab (Lablab purpureus (L.) Sweet) an underutilized tropical legume crop plays a crucial role in global food and nutritional security. To enhance our understanding of its genetic makeup towards developing elite cultivars we sequenced and assembled a draft genome of L. purpureus accession PK2022T020 using a single tube long fragment read (stLFR) technique. Results and discussion: The preliminary assembly encompassed 367 Mb with a scaffold N50 of 4.3 Mb. To improve the contiguity of our draft genome we employed a chromatin contact mapping (Hi-C) approach to obtain a pseudochromosome-level assembly containing 366 Mb with an N50 length of 31.1 Mb. A total of 327.4 Mb had successfully been anchored into 11 pseudomolecules corresponding to the haploid chromosome number in lablab. Our gene prediction recovered 98.4% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Comparative analyses utilizing sequence information from single-copy orthologous genes demonstrated that L. purpureus diverged from the last common ancestor of the Phaseolus/Vigna species approximately 27.7 million years ago. A gene family expansion analysis revealed a significant expansion of genes involved in responses to biotic and abiotic stresses. Our high-quality chromosome-scale reference assembly provides an invaluable genomic resource for lablab genetic improvement and future comparative genomics studies among legume species. Copyright ? 2024 Pootakham Somta Kongkachana Naktang Sonthirod U-Thoomporn Yoocha Phadphon and Tangphatsornruang.
Keyword
annotation | chromosome-scale | genome assembly | Hi-C | Lablab purpureus
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
License
CC BY
Rights
Authors
Publication Source
WOS