Biology subjects

Knowles, L. S.

Publications and source records attributed to Knowles, L. S..

3 recordsLinked to original sources

bioRxiv2026

Genome Report: Long read, high-coverage reference genomes of the Nymphalid butterflies Catonephele acontius and C. numilia (Nymphalidae: Biblidinae)

Withdrawal StatementThe authors have withdrawn this manuscript because in February 2026, the authors found that the Catonephele numilia specimen was misidentified and was in fact also Catonephele acontius. Thus, the data in the article describing the Catonephele numilia genome is invalid, as it in fact describes a second Catonephele acontius genome. This data invalidation has resulted in a loss of confidence in the results and conclusions reported in the article as far as they apply to Catonephele numilia. The data describing Catonephele acontius is not affected and remains valid. The authors are, therefore, retracting this article. All authors agree with the retraction. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

genomics↗

bioRxiv2025

A high-quality draft genome assembly of the Neotropical butterfly, Batesia hypochlora (Nymphalidae: Biblidinae)

We report a long-read high-coverage reference genome assembly of the Neotropical butterfly, Batesia hypochlora (Nymphalidae: Biblidinae). This represents the first reference genome in the Biblidinae subfamily, a clade subject to ongoing studies on seasonal and climate adaptation in the Amazon. We assembled the genome from PacBio HiFi long reads (66X coverage), polished it with Illumina short reads (15X coverage), and annotated it using PacBio IsoSeq RNA data. We observed 15 chromosome-sized scaffolds varying in length from 13.2 Mbp to 37.6 Mbp (median 24.3 Mbp), combining a total genome size of 395.788 Mbp. This assembly is highly contiguous (contig N50 of 25.14 Mbp) and complete (BUSCO completeness score of 98.6% and 0.2% duplication rate). Repeat annotation revealed that the genome consists of about one-third transposable elements. Gene prediction using RNAseq evidence uncovered 19,395 genes, of which 17,400 were assigned to 2,883 orthogroups when including genomes of the fruitfly, silk moth, and three other Nymphalid butterfly species. The high sequencing depth also allowed us to assemble the genomes of the mitochondria and the common endosymbiotic bacterium Wolbachia. The mitochondrial genome was fully assembled (15,540 bp in size) with all expected genes annotated. The Wolbachia genome was fragmented, and we determined that it belongs to the B-supergroup. The high-quality assembly of B. hypochlora can represent the subfamily in further comparative analysis of evolution and provide a key resource for ongoing work to explore reproductive biology and adaptations to seasonality in Amazonian butterflies.

genomics↗

bioRxiv2023

Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution

Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly-available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping efforts that rely on repetitive elements as sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimise primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes. SignificanceAmphibians display more variation in genome size than any other vertebrate lineage. Complexities associated with large genomes frequently hamper genome assembly and population genetic studies. Here we use long-read HiFi sequences to generate a high-quality 6.3 Gbp genome assembly of the poison frog Dendrobates tinctorius. We use this genome and leverage comparative genomics and de novo annotations to quantify aspects of genome evolution driven by repetitive transposable genetic elements. Our results provide support for the dynamic role that transposable elements play in driving the evolution of "genomic gigantism" in amphibians. We also show how transposable elements can be leveraged for cost-efficient population genetic studies using limited input material.

genetics↗