Genome of the Lord Howe Island Stick Insect Reveals a Highly Conserved Phasmid X Chromosome

Stuart, Oliver; Cleave, Rohan; Magrath, Michael J. L.; Mikheyev, Sasha

doi:10.1093/gbe/evad104

Cited by 5 publications

(5 citation statements)

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“…It can be argued that complete dosage compensation should refer to situations where the single X is transcribed at a level comparable to the ancestral levels for two X copies, prior to X chromosome formation (i.e., when the X chromosome would have been an autosome; [52]). However, the X chromosome in stick insects has been conserved for at least 120 Mya [13,53] and shares most of its content with the X chromosome in other insect orders that diverged over 450 million years ago [15], making it impossible to infer ancestral transcription levels. Why X-linked genes are overall less expressed than autosomal genes in Timema remains an open question.…”

Section: Figure 1 Complete Dosage Compensation In Male Somatic Tissue...mentioning

confidence: 99%

Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development

Djordjevic,

Tran Van,

Toubiana

et al. 2024

Preprint

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Differentiated sex chromosomes are frequently associated with major transcriptional changes: the evolution of dosage compensation (DC) to equalize gene expression between the sexes and the establishment of meiotic sex chromosome inactivation (MSCI). Our study investigates the mechanisms and developmental dynamics of dosage compensation and meiotic sex chromosome inactivation in the stick insect speciesT. poppense. Stick insects are characterized by XX/XO sex determination and an X chromosome which likely evolved prior to the diversification of insects over 450 Mya. We generated a chromosome-level genome assembly and analyzed gene expression from various tissues (brain, gut, antennae, leg, and reproductive tract) across developmental stages in both sexes. Our results show that complete dosage compensation is maintained in male somatic tissues throughout development, mediated by upregulation of the single X chromosome. Contrarily, in male reproductive tissues, dosage compensation is present only in the early nymphal stages. As males reach the 4th nymphal stage and adulthood, X-linked gene expression diminishes, coinciding with the onset of MSCI. This reduction is associated with histone modifications indicative of transcriptional silencing, aligning with meiotic progression. These findings reveal the dynamic regulation of X-linked gene expression inT. poppense, and suggest that reduced X-expression in insect testes is generally driven by MSCI rather than an absence of dosage compensation mechanisms. Our work provides critical insights into sex chromosome evolution and the complex interplay of dosage compensation and MSCI across tissues and developmental stages.

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Section: Figure 1 Complete Dosage Compensation In Male Somatic Tissue...mentioning

confidence: 99%

Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development

Djordjevic,

Tran Van,

Toubiana

et al. 2024

Preprint

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“…Sequence data was delivered demultiplexed with adapters trimmed. Reads were aligned to the reference genome (Stuart et al, 2023) with bwa mem v0.7.17 (Li, 2013) and PCR duplicates removed with the samtools v1.12 markdup subroutine (Li et al, 2009). Mapping statistics are presented in Supplementary Table 1.…”

Section: Whole-genome Resequencingmentioning

confidence: 99%

“…We retained homozygous reference calls in the resultant vcf file in order to correctly calculate genome-wide heterozygosity later. We filtered genotype calls first by removing any site falling into known repeat regions (Stuart et al, 2023) and then removed all indels. Finally, we used vcflib v1.…”

Section: Analysis Of High-coverage Sequence Datamentioning

confidence: 99%

“…We identified segregating sites within populations and fixed diZerences between populations. First, we used the -doMaf subroutine of angsd to obtain per-site estimates of minor allele frequency across the autosomes excluding regions masked by RepeatMasker (Smit et al, 2021) (see Stuart et al (2023) for a description of the repeat identification process).…”

Section: Identifying Polymorphic Sites and Accounting For Assembly Errormentioning

confidence: 99%

“…The annotations used here are of varying quality, indicated by the low BUSCO score of the protein annotations (Stuart et al, 2023). It is possible that some of our results may be driven by low-quality annotations.…”

Section: Characterising Deleterious Mutation Loadmentioning

confidence: 99%

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Purging of highly deleterious alleles through an extreme bottleneck

Stuart,

Cleave,

Pearce

et al. 2024

Preprint

Self Cite

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Transitions to captivity are usually population bottlenecks and so may contribute to the fitness decline of captive-bred species by genetic drift and increased inbreeding. Purging can remove deleterious alleles from populations during declines and bottlenecks but the strength of this effect across different scenarios is unknown. The Lord Howe Island stick insect,Dryococelus australis, has been bred in captivity since 2003 and passed through an extreme bottleneck: only two mating pairs with only one new addition since then. We document extremely low heterozygosity and high inbreeding in the wild, suggestive of low population size and/or a recent colonisation bottleneck. We then test the ability of natural selection to purge deleterious alleles following an extreme population bottleneck by comparing patterns of genetic diversity in wild and captive-bredD. australis. Captive-bred individuals had lower heterozygosity and a greater number of long runs-of-homozygosity compared to wild individuals, implying strong inbreeding in captivity which would facilitate purging. Highly deleterious alleles were preferentially depleted in captivity but all other alleles, coding and non-coding, had the same mean frequency change in captivity compared to the wild. The more deleterious an allele was predicted to be, the more likely it was found outside of runs-of-homozygosity. These results are consistent with inbreeding purging these deleterious alleles. We show that purging can operate on highly deleterious alleles via inbreeding, even after an extreme bottleneck. This may contribute to the persistence of captive populations, although strong drift will also limit their adaptive potential in the future, in captivity and once reintroduced into the wild.

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An unusually large genome from an unusually large stonefly: A chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae)

Eichert,

Sproul,

Tolman

et al. 2024

Journal of Heredity

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Pteronarcys californica (Newport 1848) is commonly referred to as the giant salmonfly and is the largest species of stonefly (Insecta: Plecoptera) in the western United States. Historically, it was widespread and abundant in western rivers, but populations have experienced a substantial decline in the past few decades, becoming locally extirpated in numerous rivers in Utah, Colorado, and Montana. Although previous research has explored the ecological variables conducive to the survivability of populations of the giant salmonfly, a lack of genomic resources hampers exploration of how genetic variation is spread across extant populations. To accelerate research on this imperiled species, we present a de novo chromosomal-length genome assembly of P. californica generated from PacBio HiFi sequencing and Hi-C chromosome conformation capture. Our assembly includes 14 predicted pseudo chromosomes and 98.8% of Insecta universal core orthologs. At 2.40 gigabases, the P. californica assembly is the largest of available stonefly assemblies, highlighting at least 9.5-fold variation in assembly size across the order. Repetitive elements (REs) account for much of the genome size increase in P. californica relative to other stonefly species, with the content of Class I retroelements alone exceeding the entire assembly size of all but two other species studied. We also observed preliminary suborder-specific trends in genome size that merit testing with more robust taxon sampling.

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Genome of the Lord Howe Island Stick Insect Reveals a Highly Conserved Phasmid X Chromosome

Cited by 5 publications

References 50 publications

Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development

Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development

Purging of highly deleterious alleles through an extreme bottleneck

An unusually large genome from an unusually large stonefly: A chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae)

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