Pootakham Wirulda, Somta Prakit, Kongkachana Wasitthee, Naktang Chaiwat, Sonthirod Chutima, U-Thoomporn Sonicha, Yoocha Thippawan, Phadphon Poompat, Tangphatsornruang Sithichoke
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.
Front Plant Sci. 2024 Mar 5;15:1347744. doi: 10.3389/fpls.2024.1347744. eCollection 2024.
Lablab ( (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 accession PK2022T020 using a single tube long fragment read (stLFR) technique.
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 diverged from the last common ancestor of the 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.
饭豆（Lablab purpureus (L.) Sweet）是一种未得到充分利用的热带豆科作物，在全球粮食和营养安全中发挥着关键作用。为了加深我们对其基因组成的理解以培育优良品种，我们使用单管长片段读取（stLFR）技术对编号为PK2022T020的种质进行了基因组测序和组装。
初步组装的基因组大小为367 Mb，支架N50为4.3 Mb。为了提高我们草图基因组的连续性，我们采用了染色质接触图谱（Hi-C）方法，获得了一个假染色体水平的组装体，大小为366 Mb，N50长度为31.1 Mb。共有327.4 Mb成功锚定到11条假分子上，对应于饭豆的单倍体染色体数。基于基准通用单拷贝直系同源基因（BUSCO）分析，我们的基因预测找回了98.4%的高度保守直系同源基因。利用单拷贝直系同源基因的序列信息进行的比较分析表明，饭豆大约在2770万年前从该物种的最后一个共同祖先分化而来。基因家族扩张分析显示，参与生物和非生物胁迫反应的基因有显著扩张。我们高质量的染色体水平参考组装为饭豆的遗传改良以及未来豆科物种间的比较基因组学研究提供了宝贵的基因组资源。
