Biology subjects

Walters, J. R.

Publications and source records attributed to Walters, J. R..

9 recordsLinked to original sources

bioRxiv2026

Wrong but useful: Bombyx silkworm W chromosome assemblies are flawed but still capture strongly reduced diversity of repetitive DNA

Degenerate sex chromosomes (e.g., the Y or W) remain among the most difficult regions of eukaryotic genomes to assemble because they are highly repetitive and structurally complex. While many recent lepidopteran genome assemblies contain W chromosome scaffolds, the accuracy and consistency of these assemblies remain uncertain, due to lack of replication within species. However, the silkworm moth Bombyx mori is an exception, with numerous independent W chromosome assemblies currently available. We compared six independent long-read W chromosome assemblies, which proved to be highly inconsistent in structure, even among nominally identical genotypes. In contrast, autosomes and the Z chromosome were highly concordant among these assemblies, indicating that current assemblies remain unreliable for resolving W chromosome structure. Additionally, we analyzed repetitive DNA content across the genome. First, we combined assembly- and read-based repeat-discovery methods to generate a comprehensive and curated Bombyx repeat library, which we make publicly available. Assessing repeat content and diversity, we find that the W chromosome is comprised almost entirely of repetitive DNA but that the richness and divergence of W repeats are substantially reduced compared to the remainder of the genome. This reduced diversity, initially inferred from assemblies, is confirmed by direct analysis of PacBio HiFi sequencing reads partitioned by chromosome. We also demonstrate that the B. mori p50ma genome assembly (the current NCBI RefSeq assembly) carries a W chromosome and mitochondrial genome introgressed from B. mandarina. This discovery provided an opportunity to investigate patterns of divergence between closely related W haplotypes, revealing substantially more rapid turnover of repeat content on the W than elsewhere in the genome. Together, our results show that current W chromosome assemblies, although structurally flawed, nevertheless capture robust biological patterns of repeat diversity and support the hypothesis that rapid repeat turnover, rather than frequent chromosome replacement, may underlie the apparent lack of W chromosome homology across Lepidoptera.

genomics↗

bioRxiv2025

Comparative Transcriptomic Analysis of Embryonic Stem Cells (ESCs) across Mammalian Species

Pluripotency, the ability of cells to self-renew and differentiate into all the cell types in an animals body, is vital for mammalian early development. This study presented a comprehensive comparative transcriptomic analysis of embryonic stem cells across multiple mammalian species, defining their progression through expanded/extended, naive, formative, and primed pluripotency states. Our findings revealed both conserved and species-specific mechanisms underlying pluripotency regulation. We also emphasized the limitations of existing state-specific markers and their limited cross-species applicability, while identifying de novo pluripotency markers that can inform future research. Despite variability in gene expression dynamics, gene co-expression networks showed remarkable conservation across species. Among pluripotency states, the primed state demonstrated the highest conservation, evidenced by shared markers, preserved gene networks, and stronger selective pressures acting on its genes. These findings provide critical insights into the evolution and regulation of pluripotency, laying a foundation for refining stem cell models to enhance their translational potential in regenerative medicine, agriculture, and conservation biology.

genomics↗

bioRxiv2023

Ghost W chromosomes and unique genome architecture in ghost moths of the family Hepialidae

The classical model of sex chromosome evolution has been recently challenged in moths and butterflies (Lepidoptera). According to the current hypothesis, the adoption of a supernumerary chromosome may have driven the transition from the Z0 to the WZ sex chromosome system in females. However, the evolutionary history of the W chromosome remains enigmatic, especially in the early-diverging lepidopteran lineages. In ghost moths of the family Hepialidae, one of the most basal lepidopteran clades, there is conflicting evidence regarding their sex chromosomes. In this study, we aimed to clarify the status of the hepialid W chromosome. Using cytogenetics and genomics, we investigated the karyotype, sex chromosomes, genome size and repeatome of multiple ghost moth species and reconstructed basic phylogenetic relationships in the group. Our data show that Hepialidae have unusually large genomes (reaching up to 1C = 3 Gb) and are the oldest known lepidopteran clade with a W chromosome. However, the W does not form a typical heterochromatin body in polyploid nuclei, known as sex chromatin, previously employed to detect the presence of W chromosomes across Lepidoptera. Moreover, in some species, the W does not exhibit distinct repeat content and can escape detection via methods that rely on W-specific sequences. Analysis of the Z chromosome confirmed highly conserved gene content, arguing for a possible origin of the hepialid W chromosome from a B chromosome. We hypothesize that the mechanism underlying the formation of sex chromatin could be used in future research to study the origin of the W chromosome.

genomics↗

bioRxiv2023

Genome sequence of Ophryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals

Apicomplexa are ancient and diverse organisms which have been poorly characterized by modern genomics. To better understand the evolution and diversity of these single-celled eukaryotes, we sequenced the genome of Ophryocystis elektroscirrha, a parasite of monarch butterflies, Danaus plexippus. The genome is miniscule, totaling only 9 million bases and containing fewer than 3,000 genes. We then compared this new sequence to the two other sequenced invertebrate-infecting apicomplexans, Porospora gigantea and Gregarina niphandrodes, which have nearly twice the gene content and found that O. elektroscirrha shares different orthologs with each sequenced relative, suggesting the true set of universally conserved apicomplexan genes is very small indeed. We investigated sequenced reads from other potential hosts to explore the viability of in silico infection screening. We recovered a similarly sized parasite genome from another butterfly, Danaus chrysippus, that was highly diverged from the O. elektroscirrha reference, possibly representing a distinct species. Using these two new genomes, we investigated potential evolutionary response by parasites to toxic phytochemicals their hosts ingest and sequester. Monarch butterflies are well-known to tolerate toxic cardenolides thanks to changes in the sequence of their Type II ATPase sodium pumps. We show that Ophryocystis completely lacks Type II or Type 4 sodium pumps, and related proteins PMCA calcium pumps show extreme sequence divergence compared to other Apicomplexa, demonstrating new avenues of research opened by genome sequencing of non-model Apicomplexa. Author SummaryThere are many relatives of Plasmodium, the single-celled parasites responsible for malaria, and they infect a wide range of animals, including insects. These parasites have received less attention however, leaving much unknown about them. We sequenced the genome of one such parasite, Ophryocystis elektroscirrha (OE), to compare it to better-studied parasites and shed light on OEs interaction with its host, the monarch butterfly. We found that OE has a tiny genome with the fewest genes of any sequenced parasite in this group, lacking many genes found in its relatives. Using our new data, we also discovered evidence that infections of other butterfly species that have been attributed to OE may be caused by a previously undiscovered distinct parasite species. And finally, we explored the evolution of a family of genes that may be targeted by medicinal plant compounds in the monarch butterflys diet; OE has lost one of these genes and radically changed the sequence of another, setting a direction for future research.

genomics↗

bioRxiv2020

ZZ Top: faster and more adaptive Z chromosome evolution in two Lepidoptera

The rate of divergence for Z or X chromosomes is theoretically predicted to be greater than autosomes, but the possible explanations for this pattern vary, as do empirical results from diverse taxa. Even among moths and butterflies (Lepidoptera), which generally share a single-origin Z chromosome, the handful of available studies give mixed support for faster or more adaptive evolution of the Z chromosome, depending on the species assayed. Here, we examine the molecular evolution of Z chromosomes in two additional lepidopteran species: the Carolina sphinx moth and the monarch butterfly, the latter of which possesses a recent chromosomal fusion yielding a segment of newly Z-linked DNA. We find evidence for both faster and more adaptive Z chromosome evolution in both species, though this effect is strongest in the neo-Z portion of the monarch sex chromosome. The neo-Z is less male-biased than expected of a Z chromosome, and unbiased and female-biased genes drive the signal for adaptive evolution here. Together these results suggest that male-biased gene accumulation and haploid selection have opposing effects on long-term rates of adaptation and may help explain the discrepancies in previous findings as well as the repeated evolution of neo-sex chromosomes in Lepidoptera.

evolutionary biology↗

bioRxiv2019

Population genomics reveals complex patterns of immune gene evolution in monarch butterflies (Danaus plexippus)

Immune genes presumably rapidly evolve as pathogens exert strong selection pressures on host defense, but the evolution of immune genes is also constrained by trade-offs with other biological functions and shaped by the environmental context. Thus, immune genes may exhibit complex evolutionary patterns, particularly when organisms disperse to or live in variable environments. We examined the evolutionary patterns of the full set of known canonical immune genes within and among populations of monarch butterflies (Danaus plexippus), and relative to a closely related species (D. gilippus). Monarchs represent a system with a known evolutionary history, in which North American monarchs dispersed to form novel populations across the world, providing an opportunity to explore the evolution of immunity in the light of population expansion into novel environments. By analyzing a whole-genome resequencing dataset across populations, we found that immune genes as a whole do not exhibit consistent patterns of selection, differentiation, or genetic variation, but that patterns are specific to functional classes. Species comparisons between D. plexippus and D. gilippus and analyses of monarch populations both revealed consistently low levels of genetic variation in signaling genes, suggesting conservation of these genes over evolutionary time. Modulation genes showed the opposite pattern, with signatures of relaxed selection across populations. In contrast, recognition and effector genes exhibited less consistent patterns. When focusing on genes with exceptionally strong signatures of selection or differentiation, we also found population-specific patterns, consistent with the hypothesis that monarch populations do not face uniform selection pressures with respect to immune function.

evolutionary biology↗

bioRxiv2019

Transcriptomics of monarch butterflies (Danaus plexippus) reveals strong differential gene expression in response to host plant toxicity, but weak response to parasite infection

Herbivorous insects have evolved many mechanisms to overcome plant chemical defenses, including detoxification and sequestration. Herbivores may also use toxic plants to reduce parasite infection. Plant toxins could directly interfere with parasites or could enhance endogenous immunity. Alternatively, plant toxins could favor down-regulation of endogenous immunity by providing an alternative (exogenous) defense against parasitism. However, studies on genome-wide transcriptomic responses to plant defenses and the interplay between host plant toxicity and parasite infection remain rare. Monarch butterflies (Danaus plexippus) are specialist herbivores that feed on milkweeds (Asclepias spp.), which contain toxic cardenolides. Monarchs have adapted to cardenolides through multiple resistance mechanisms and can sequester cardenolides to defend against bird predators. In addition, high-cardenolide milkweeds confer medicinal effects to monarchs against a specialist protozoan parasite (Ophryocystis elektroscirrha). We used this system to study the interplay between the effects of plant toxicity and parasite infection on global gene expression. Our results demonstrate that monarch larvae differentially express several hundred genes when feeding on A. curassavica and A. incarnata, two species that are similar in nutritional content but differ substantially in cardenolide concentrations. These differentially expressed genes include genes within multiple families of canonical insect detoxification genes, suggesting that they play a role in monarch toxin resistance and sequestration. Interestingly, we found little transcriptional response to infection. However, parasite growth was reduced in monarchs reared on A. curassavica, and in these monarchs, a small number of immune genes were down-regulated, consistent with the hypothesis that medicinal plants can reduce reliance on endogenous immunity.

genomics↗

bioRxiv2018

A complex copy number variant underlies differences in both colour plumage and cold adaptation in a dimorphic seabird.

Colour morphs associated with different physiological adaptations offer unique opportunities to study the genomic basis of otherwise elusive adaptive traits. These complex balanced polymorphisms are often controlled by groups of tightly linked genes, and understanding how these supergenes evolve and are maintained is an active area of research in evolutionary biology (Schwander et al. 2014, Thompson and Jiggins 2014). Within the Atlantic, the common murre (Uria aalge, a colonial seabird) displays a plumage colour dimorphism ( bridled and unbridled) that seems to be associated with differences in thermal adaptation (Birkhead 1984; Reiertsen et al. 2012). The genes associated with bridling and how these genes affect thermal adaptation are unknown. Using whole genome resequencing, we investigate the genomic basis of differences in colouration and thermal adaptation between the two morphs, and how the association between the two traits is maintained despite random mating. We identify a 60 kb genomic region of high differentiation laying in the intergenic area amongst three candidate genes for colouration and thermal adaptation: retinoic acid receptor beta (RARB), thyroid hormone receptor beta (THRB), and nuclear receptor subfamily 1 group D member 2 (NR1D2 or Rev-erb{beta}). Differentiation is due to a complex copy number variant (CNV) that suppresses recombination locally. We show that this CNV acts as a supergene and maintain association between regulatory elements likely affecting gene expression of one or more of the identified candidate genes. Our analyses also provide insights into the origin of the dimorphism: while copy number proliferation in the unbridled haplotype was potentially mediated by transposable elements (TEs), the bridled haplotype seems to have introgressed from the more cold-adapted sister species, the thick-billed murre (U. lomvia). Our results highlight the role of copy number variants in adaptation, especially when association among traits is maintained in the face of gene flow. They also shed light into the molecular mechanisms of adaptive thermogenesis in birds, which is poorly understood.\n\nHighlightsO_LIDifferences in plumage colour in Atlantic common murres are associated with different thermal adaptations\nC_LIO_LIA single region is highly differentiated between bridled and unbridled morphs\nC_LIO_LIA complex copy number variant in a non-coding region underlies the dimorphism\nC_LIO_LITransposable elements and adaptive introgression from the thick-billed murre seem to explain the origin of the dimorphism\nC_LI

evolutionary biology↗

bioRxiv2018

Adaptive evolution of sperm proteins depends on sperm competition in a pair of Lepidoptera

Recent theory posits that adaptive evolution of reproductive proteins should depend on rates of female remating. In particular, selection on reproductive proteins is proposed to be weak unless females remate frequently, in which case cryptic female choice and sperm competition impose stronger selection. Here, we test these predictions by explicitly examining the role of selection in the molecular evolution of sperm genes in Lepidoptera, the butterflies and moths. Males of this order produce both fertilizing eupyrene sperm and a secondary apyrene type that lacks DNA. Based on population genetic analyses in two species, the monandrous Carolina sphinx moth and the highly polyandrous monarch butterfly, we see evidence for increased selection in fertilizing sperm, but only in the polyandrous species. This signal comes primarily from a decrease in non-synonymous polymorphism in sperm proteins compared to the rest of the genome, indicative of strong purifying selection. Investigation of the distribution of fitness effects of new non-synonymous mutations in monarch sperm confirms stronger selection on sperm proteins in monarchs, with very few neutral variants and weakly deleterious variants and a preponderance of strongly deleterious variants. Additionally, sperm genes in the monarch show an elevation of beneficial variants compared to the rest of the genome, suggesting a role for increased positive selection. Our results suggest that sperm competition can be a powerful selective force at the sequence level as well.

evolutionary biology↗