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The full text of this article can be freely accessed on the publisher's website

Table_1_A de novo chromosome-scale assembly of the Lablab purpureus genome.xlsx

IntroductionLablab (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 discussionThe 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.</p

DataSheet_1_A de novo chromosome-scale assembly of the Lablab purpureus genome.pdf

IntroductionLablab (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 discussionThe 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.</p

Analysis of synonymous and non-synonymous changes in cassava SNPs.

<p>Detailed information regarding the changes introduced by nucleotide substitutions and their distribution according to the nucleotide position within codons.</p><p>Analysis of synonymous and non-synonymous changes in cassava SNPs.</p

Manhattan plot of QTL LOD scores for starch viscosity traits.

<p>The Manhattan plots display the LOD scores of SNP markers along each linkage group (designated at the bottom). The red and orange lines indicated genome-wide and chromosome-wide significance thresholds, respectively.</p

Large-Scale SNP Discovery through RNA Sequencing and SNP Genotyping by Targeted Enrichment Sequencing in Cassava (<i>Manihot esculenta</i> Crantz)

<div><p>Cassava (<i>Manihot esculenta</i> Crantz) is one of the most important crop species being the main source of dietary energy in several countries. Marker-assisted selection has become an essential tool in plant breeding. Single nucleotide polymorphism (SNP) discovery via transcriptome sequencing is an attractive strategy for genome complexity reduction in organisms with large genomes. We sequenced the transcriptome of 16 cassava accessions using the Illumina HiSeq platform and identified 675,559 EST-derived SNP markers. A subset of those markers was subsequently genotyped by capture-based targeted enrichment sequencing in 100 F₁ progeny segregating for starch viscosity phenotypes. A total of 2,110 non-redundant SNP markers were used to construct a genetic map. This map encompasses 1,785 cM and consists of 19 linkage groups. A major quantitative trait locus (QTL) controlling starch pasting properties was identified and shown to coincide with the QTL previously reported for this trait. With a high-density SNP-based linkage map presented here, we also uncovered a novel QTL associated with starch pasting time on LG 10.</p></div

Distribution of SNP markers on the linkage groups.

<p>Distribution of SNP markers on the linkage groups.</p

High-density genetic map of cassava.

<p>The SNP-based map included 2,110 non-redundant markers distributed over 19 linkage groups (LGs). The length of the each linkage group (in cM) was indicated at the bottom.</p

Statistics for RNA-seq data from 16 cassava accessions.

<p>Quality scores measure the probability that the base is called incorrectly. Quality scores of 20 (Q20) represent a corresponding call accuracy of 99%.</p><p>Statistics for RNA-seq data from 16 cassava accessions.</p