Biology subjects

Kersey, P.

Publications and source records attributed to Kersey, P..

5 recordsLinked to original sources

bioRxiv2025

AI-based prediction of herbarium sequencing success across the plant tree of life

DNA recovered from herbarium specimens represents a vital asset in botanical research, playing a pivotal role in unravelling the evolution, diversity, and ecological dynamics of plants. Despite its importance, challenges such as fragmented DNA and insufficient sequencing yields render molecular data retrieval a high-risk and costly endeavour involving the use of non-replaceable herbarium specimens. Here, we propose a framework based on Artificial Intelligence (AI) to forecast the success of genomic DNA extraction suitable for sequencing from herbarium samples. Our model integrates morphological characteristics and sample colour derived from scanned herbarium images, metadata including sample age and locality, and DNA quantity measurements of samples. We train a deep learning algorithm with ca. 2,000 specimens that have been digitized and sequenced in the framework of the Plant and Fungal Trees of Life (PAFTOL) Project, spanning from year 1832 to the present. As training datasets increase with ongoing digitization and genomic sequencing efforts, our AI predictive model can support researchers in selecting the herbarium samples with the highest likelihood of yielding high-quality genomic DNA from amongst a vast array of globally distributed candidate specimens. Our approach enhances the contribution of herbarium-derived DNA in large-scale studies and facilitates the utilisation of historical collections for a deeper understanding of plant evolution and ecology, with implications for conservation.

plant biology↗

bioRxiv2024

Towards an unbiased characterization of genetic polymorphism

Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to provide nearly complete genome sequences for population samples, should solve the problem--except that characterizing and making sense of non-SNP variation is difficult even with perfect sequence data. Here we analyze 27 genomes of Arabidopsis thaliana in an attempt to address these issues, and illustrate what can be learned by analyzing whole-genome polymorphism data in an unbiased manner. Estimated genome sizes range from 135 to 155 Mb, with differences almost entirely due to centromeric and rDNA repeats that are difficult to assemble. The completely assembled chromosome arms comprise roughly 120 Mb in all accessions, but are full of structural variants, largely due to transposable elements. Even with only 27 accessions, a pan-genome coordinate system that includes the resulting variation ends up being [~] 70% larger than the size of any one genome. Our analysis reveals an incompletely annotated mobile-ome: we not only detect several novel TE families, but also find that existing TE annotation is a poor predictor of elements that have recently been active. In contrast to this, the genic portion, or "gene-ome", is highly conserved. By annotating each genome using accession-specific transcriptome data, we find that 13% of all (non-TE) genes are segregating in our 27 accessions, but most of these are transcriptionally silenced. Finally, we show that with short-read data we previously massively underestimated genetic variation of all kinds, including SNPs--mostly in regions where short reads could not be mapped reliably, but also where reads were mapped incorrectly. We demonstrate that SNP-calling errors can be biased by the choice of reference genome, and that RNA-seq and BS-seq results can be strongly affected by mapping reads only to a reference genome rather than to the genome of the assayed individual. In conclusion, while whole-genome polymorphism data pose tremendous analytical challenges, they also have the potential to revolutionize our understanding of genome evolution.

genomics↗

bioRxiv2021

The salmon louse genome: copepod features and parasitic adaptations.

Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod. We present the 695.4 Mbp L. salmonis genome assembly containing {approx}60% repetitive regions and 13081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics validated annotation and revealed a marked shift in gene expression after host attachment, including downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of peroxisomes, numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite large capacity to develop resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.

genomics↗

bioRxiv2018

The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for Bluetongue virus

BackgroundThe use of the new genomic technologies has led to major advances in control of several arboviruses of medical importance such as Dengue. However, the development of tools and resources available for vectors of non-zoonotic arboviruses remains neglected. Biting midges of the genus Culicoides transmit some of the most important arboviruses of wildlife and livestock worldwide, with a global impact on economic productivity, health and welfare. The absence of a suitable reference genome has hindered genomic analyses to date in this important genus of vectors. In the present study, the genome of Culicoides sonorensis, a vector of bluetongue virus (BTV) in the USA, has been sequenced to provide the first reference genome for these vectors. In this study, we also report the use of the reference genome to perform initial transcriptomic analyses of vector competence for BTV.\n\nResultsOur analyses reveal that the genome is 197.4 Mb, assembled in 7,974 scaffolds. Its annotation using the transcriptomic data generated in this study and in a previous study has identified 15,629 genes. Gene expression analyses of C. sonorensis females infected with BTV performed in this study revealed 165 genes that were differentially expressed between vector competent and refractory females. Two candidate genes, glutathione S-transferase (gst) and the antiviral helicase ski2, previously recognized as involved in vector competence for BTV in C. sonorensis (gst) and repressing dsRNA virus propagation (ski2), were confirmed in this study.\n\nConclusionsThe reference genome of C. sonorensis has enabled preliminary analyses of the gene expression profiles of vector competent and refractory individuals. The genome and transcriptomes generated in this study provide suitable tools for future research on arbovirus transmission. These provide a significant resource for these vector lineage, which diverged from other major Dipteran vector families over 200 million years ago. The genome will be a valuable source of comparative data for other important Dipteran vector families including mosquitoes (Culicidae) and sandflies (Psychodidae), and yield potential targets for transgenic modification in vector control and functional studies.

genomics↗

bioRxiv2017

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum functional genome and evolutionary origin of diatoms

Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery for the first time of extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping which increases the diversity of transcripts to regulate gene expression in response to nutrient limitations. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.

bioinformatics↗