Biology subjects

Davalan, T.

Publications and source records attributed to Davalan, T..

2 recordsLinked to original sources

bioRxiv2026

Chromosome-level, haplotype-resolved genome assembly of the tanniferous forage legume big trefoil (Lotus pedunculatus Cav.) using CiFi

Big trefoil (Lotus pedunculatus Cav.) is a perennial forage legume that thrives on acidic, low-fertility soils and produces condensed tannins that reduce enteric methanogenesis in ruminants. Despite this agronomic potential, genomic resources for the species remain scarce, and the existing haploid assembly does not resolve the two haplotypes of this outcrossing diploid species. Here we present a haplotype-resolved, chromosome-level reference genome for L. pedunculatus genotype Lusitano29 -- the first plant genome assembled using CiFi, a long-read chromosome conformation capture method. We combined PacBio HiFi long reads with CiFi concatemers produced from DpnII and HindIII libraries; in silico digestion and combinatorial pairing of the resulting monomers yielded 790.3 M and 10.3 M pseudo-paired contacts, respectively, enabling scaffolding and manual curation to chromosome level. The 991.1 Mb assembly resolves two phased haplotypes of 500 and 491 Mb, with 96.6% of the sequence anchored in twelve pseudo-chromosomes (six per haplotype). Telomeric repeats were detected at 19 of 24 pseudo-chromosome ends, and no structural errors were detected (scaffold N50 73.8 Mb; consensus QV 64.7; k-mer completeness 99.4%; genome-mode BUSCO completeness 97.0%; CRAQ S-AQI 100.0). Annotation supported by PacBio Iso-Seq full-length transcripts predicted 38,069 and 36,484 protein-coding genes in haplotypes 1 and 2, respectively (protein-mode BUSCO completeness 96.5%), indicating a high completeness of annotated genes. This genome assembly provides a foundation for allele-aware trait dissection of proanthocyanidin biosynthesis, comparative genomics in Lotus, and population genomics and genomics-assisted breeding in L. pedunculatus.

genomics↗

bioRxiv2026

Chromosome-level genome assembly of the swallowtail butterfly Parides eurimedes mylotes is a valuable resource for studying wing coloration

High-quality chromosome-scale assemblies are scarce in Papilionidae. This limits comparative genomics to model species, Lepidoptera, Bombyx mori. Here, we present a phased, chromosome-level genome assembly of Parides eurimedes mylotes. We generated this assembly using 125[x] PacBio HiFi sequencing and assembled it with hifiasm. The final haplotype assemblies (Hap1 and Hap2) span 274 Mb and 270 Mb, respectively. These assemblies are organized into 31 near-telo-mere-to-telomere chromosomes, with scaffold N50 values of 9.72 Mb and 9.22 Mb, respectively. BUSCO analysis revealed assembly completeness of 96.6 % and 96.4 % for Hap1 and Hap2, respectively. Repeats annotation identified 18-19 % repetitive content, with Helitron elements being the dominant class of transposable elements. We identified the W and Z sex chromosomes and completely assembled the mitochondrial genome. Compared to the previously available Parides photinus draft assembly, our genome exhibits an 11,000-fold reduction in scaffold fragmentation and nearly complete gene assembly. This assembly provides a robust genomic reference for functional, evolutionary, and multi-omics investigation in Papilionidae. In addition to serving as a high-quality genomic reference for Papilionidae, this assembly is essential for linking the genetic architecture of butterfly wings to the hierarchical nanostructures underlying structural coloration. By identifying the genes and regulatory networks involved in scale morphogenesis, we can correlate the butterflys genotype with its photonic function. This insight into the evolutionary origin of the biological photonic systems informs the design of biomimetic, structurally colored materials.

genomics↗