Biology subjects

Martins, N. F.

Publications and source records attributed to Martins, N. F..

4 recordsLinked to original sources

bioRxiv2025

A draft genome assembly of the agricultural pest Leucoptera coffeella and analysis of its dsRNA processing machinery is a key step towards RNAi-based biopesticides in Lepidoptera

The Coffee Leaf Miner (Lepidoptera: Lyonetiidae: Leucoptera coffeella) is a specialist herbivore and major global pest of coffee plants. Current pest control strategies primarily rely on chemical pesticides, leading to human and environmental constraints. Additionally, the emergence of insecticide-resistant populations underscores the urgent need for more specific and efficient pest management strategies. The development of novel techniques for controlling this insect pest requires rigorous interrogation of its physiology and interactions with host plants at a molecular/genetic level. To enable future research in this vein, we sequenced and assembled a draft L. coffeella genome using PacBio highly accurate long-reads (HiFi). Our assembly is comprised of 1615 contigs showing fragmentation, yet the majority of gene content is represented (BUSCO complete = 91.7%). We annotated 17467 protein-coding genes within our assembly, seven of which are core components of the small interfering RNA machinery. The expression of these genes was further confirmed via qPCR. This analysis - and the underlying genomic data - highlights potential targets for RNAi-based biopesticide development and will serve as the foundation for important future research aimed at protecting global coffee production from one of its most destructive pests.

genomics↗

bioRxiv2024

Complex genomic ancestry in southern regions and drivers of continental-level genetic diversity in the wolves of Asia

Gray wolves (Canis lupus) in Asia encompass most of the species global genetic diversity and many endangered populations. However, a clear understanding of the evolutionary history of wolves from many parts of Asia, especially southern regions, is lacking. We used 98 whole genomes of wolves sampled across Eurasia to better resolve their evolutionary history by investigating phylogenetic and gene flow histories across the genome, and to characterize their demographic history and genetic diversity. The strongest barriers to gene flow coincided with boundaries separating the three major extant wolf lineages - Indian, Tibetan, and Holarctic. Wolves in the central Asian mountain ranges belonged to the Holarctic lineage, and despite their geographic adjacency only share minimal ancestry with the Tibetan lineage. In contrast, wolves from eastern Asia share population-wide ancestry with the Tibetan lineage, which may reflect an unsampled lineage similar, but not exactly to, the modern-day Tibetan lineage. Wolves from southwestern Asia also share population-wide ancestry with the Indian lineage, likely due to old (>6kya) admixture events. Long-term historical declines over the last 100,000 years, geographic isolation, and recent inbreeding have resulted in the Indian and Tibetan wolves having some of the lowest levels of genetic diversity and highest realized genetic loads. In contrast, adjacent populations exhibit some of the highest genetic diversity, due in part to admixture along contact zones. Our study illustrates how using multiple approaches that consider heterogenous signals across the genome can more fully resolve the historical and contemporary processes that have led to present-day species diversity.

evolutionary biology↗

bioRxiv2023

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf genetic affiliations and their taxonomic implications, we sequenced and analysed the genomes of a historical Korean wolf dated to the beginning of the 20th century, and a captive wolf originally located at the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find the Korean wolf has similar diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is more genetically similar to wolves from the Tibetan Plateau, hence, Korean wolf conservation programs might not benefit from the inclusion of this specimen.

evolutionary biology↗

bioRxiv2020

Systematic auditing is essential to debiasing machine learning in biology

Representational biases that are common in biological data can inflate prediction performance and confound our understanding of how and what machine learning (ML) models learn from large complicated datasets. However, auditing for these biases is not a common practice in ML in the life sciences. Here, we devise a systematic auditing framework and harness it to audit three different ML applications of significant therapeutic interest: prediction frameworks of protein-protein interactions, drug-target bioactivity, and MHC-peptide binding. Through this, we identify unrecognized biases that hinder the ML process and result in low model generalizability. Ultimately, we show that, when there is insufficient signal in the training data, ML models are likely to learn primarily from representational biases.

systems biology↗