Biology subjects

Gordon, E. R. L.

Publications and source records attributed to Gordon, E. R. L..

4 recordsLinked to original sources

bioRxiv2023

Chromosome-aware phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) elucidates ancient gene conflict

Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for non-vertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 Anchored Hybrid Enrichment [AHE], 24 RNA-Seq, and 70 whole-genome sequencing [WGS] samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g., nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse ([~]7,000 spp.) and old (>180 MYA) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade.

genomics↗

bioRxiv2022

Improved target capture with lower hybridization temperatures for invertebrate loci with different baiting strategies: a case study of the leaf-footed bugs and allies (Hemiptera: Coreoidea)

Target capture approaches are widely used in phylogenomic studies, yet only four experimental comparisons of a critical parameter, hybridization temperature, have been published. These studies provide conflicting conclusions regarding the benefits of lower temperatures during target capture, and none include invertebrates where bait-target divergences may be higher than seen in vertebrate capture studies. Most capture studies use a fixed hybridization temperature of 65{degrees}C to maximize the proportion of on-target data, but many invertebrate capture studies report low locus recovery. Lower hybridization temperatures, which might improve locus recovery, are not commonly employed in invertebrate capture studies. We used leaf-footed bugs and relatives (Hemiptera: Coreoidea) to investigate the effect of hybridization temperature on capture success of ultraconserved elements (UCE) targeted by previously published baits derived from divergent hemipteran genomes and other loci targeted by newly designed baits derived from less divergent coreoid transcriptomes. We found touchdown capture approaches with lower hybridization temperatures generally resulted in lower proportions of on-target reads and lower read depth but were associated with more contigs and improved recovery of UCE loci. Low temperatures were also associated with increased numbers of putative paralogs of UCE loci. Hybridization temperatures did not generally affect recovery of newly targeted loci, which we attributed to their lower bait-target divergences (compared to higher divergences between UCE baits and targets) and greater bait tiling density. Thus, optimizing in vitro target capture conditions to accommodate low hybridization temperatures can provide a cost-effective, widely applicable solution to improve recovery of protein-coding loci in invertebrates.

genomics↗

bioRxiv2020

New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics

Despite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, increasing rates of false positive results. Many such tools also suffer from difficult installation processes and lack adequate user resources. Here, we describe a program using freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance as well as that of other utilized bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, as well as on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated, low and high depth shotgun, and target capture assemblies as well or better than other software as assessed by finding the most genes with maximal coverage and with a low rate of false positives throughout all datasets. The software (implemented in Python), tutorials, and manual are freely available at https://github.com/AlexKnyshov/alibaseq.

bioinformatics↗

bioRxiv2018

Cost-efficient high throughput capture of museum arthropod specimen DNA using PCR-generated baits

O_LIGathering genetic data for rare species is one of the biggest remaining obstacles in modern phylogenetics, particularly for megadiverse groups such as arthropods. Next generation sequencing techniques allow for sequencing of short DNA fragments contained in preserved specimens >20 years old, but approaches such as whole genome sequencing are often too expensive for projects including many taxa. Several methods of reduced representation sequencing have been proposed that lower the cost of sequencing per specimen, but many remain costly because they involve synthesizing nucleotide probes and target hundreds of loci. These datasets are also frequently unique for each project and thus generally incompatible with other similar datasets.\nC_LIO_LIHere, we explore utilization of in-house generated DNA baits to capture commonly utilized mitochondrial and ribosomal DNA loci from insect museum specimens of various age and preservation types without the a priori need to know the sequence of the target loci. Both within species and cross-species capture are explored, on preserved specimens ranging in age from one to 54 years old.\nC_LIO_LIWe found most samples produced sufficient amounts of data to assemble the nuclear ribosomal rRNA genes and near complete mitochondrial genomes and produce well-resolved phylogenies in line with expected results. The dataset obtained can be straightforwardly combined with the large cache of existing Sanger-sequencing-generated data built up over the past 30 years and targeted loci can be easily modified to those commonly used in different taxa. Furthermore, the protocol we describe allows for inexpensive data generation (as low as [~]$35/sample), of at least 20 kilobases per specimen, for specimens at least as old as [~]1965, and can be easily conducted in most laboratories.\nC_LIO_LIIf widely applied, this technique will accelerate the accurate resolution of the Tree of Life especially on non-model organisms with limited existing genomic resources.\nC_LI

evolutionary biology↗