Title: Identification of sex chromosomes and primary sex ratio in the small hive beetle, a worldwide parasite of honey bees
Abstract BackgroundThe small hive beetle (SHB), Aethina tumida, has emerged as a worldwide threat to honey bees in the past two decades. These beetles harvest nest resources, feed on larval bees, and ultimately spoil nest resources with gelatinous slime together with the fungal symbiont Kodamaea ohmeri. ResultsHere, we present the first chromosome-level genome assembly for the SHB. With a 99.1% representation of conserved (BUSCO) arthropod genes, this resource enables the study of chemosensory, digestive, and detoxification traits critical for SHB success and possible control. We use this annotated assembly to characterize features of SHB sex chromosomes and a female-skewed primary sex ratio. We also found chromosome fusion and a lower recombination rate in sex chromosomes than in autosomes. ConclusionsGenome-enabled insights will clarify the traits that allowed this beetle to exploit hive resources successfully and will be critical for determining the causes of observed sex ratio asymmetries.  more » « less
Award ID(s):
2109306
PAR ID:
10500981
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
GigaScience
Volume:
12
ISSN:
2047-217X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Larracuente, Amanda (Ed.)
    Abstract In most animal species, the sex-determining pathway is typically initiated by the presence/absence of a primary genetic cue at a critical point during development. This primary genetic cue is often located on a single locus—referred to as sex chromosomes—and can be limited to females (in a ZZ/ZW system) or males (in an XX/XY system). One trademark of sex chromosomes is a restriction or cessation of recombination surrounding the sex-limited region (to prevent its inheritance in the homogametic sex). This may lead to—through a variety of mechanisms—higher amounts of genetic divergence within this region, ie between the X/Z and Y/W chromosomes, especially when compared with their autosomal counterparts. Recent advances in genome sequencing and computation have brought with them the ability to resolve haplotypes within a diploid individual, permitting assembly of previously challenging genomic regions like sex chromosomes. Leveraging these advances, we identified replicable diagnostic characteristics between typical autosomes and sex chromosomes (within a single genome assembly). Under this framework, we can use this information to identify putative sex chromosome linkage groups across divergent vertebrate taxa and simultaneously curate misassembled regions on autosomes. Here, we present this conceptual framework and associated tool for identifying candidate sex chromosome linkage groups from a single, diploid individual dubbed Sex Chromosome Identification by Negating Kmer Densities. 
    more » « less
  2. Wheat, Christopher (Ed.)
    Abstract Onthophagus binodis is a coprophagous scarab beetle native to southern Africa. This species and many others in the tribe Onthophagini have been introduced to farms across multiple continents in the context of cattle pasture management efforts. The ecosystem services provided by this species, along with the amenability of comparative developmental and evolutionary studies in this clade, contribute to its role as an emerging insect model system. Here, we present sex-specific chromosomal-level genome assemblies for O. binodis generated from a combination of PacBio long reads and HiC chromatin conformation sequencing. The completeness of the 950.5 Mb female assembly and the 880.5 Mb male assembly is indicated by a contig length N50 of at least 58.6 Mb. BUSCO single-copy and duplicated completeness scores were 99.0% and 0.9% for the female assembly and 97.4% and 2.1% for the male assembly. Gene modeling identified at least 15,403 gene models in each genome with an average transcript length of 1.6 kb. Comparative analyses with other Onthophagini genomes indicated a dramatic expansion of repetitive sequences, which now comprise over 75% of this species’ genome and have driven the expansion of overall genome size to nearly twice that of close relatives. We combined the best-assembled chromosome-scale scaffolds from each sex to generate a hybrid reference assembly for this species. Comparative genomic analyses show that the nine autosomes and the X chromosome identified here in O. binodis are likely conserved throughout Onthophagini. Our sex-specific sequencing approach allowed us to identify putative Y chromosome sequences in the male assembly via coverage mapping and k-mer abundance comparisons. These genomes will be of great value to the scientific community as resources for studying insect genome evolution, development, and ecology. 
    more » « less
  3. Abstract Climatic and soil features influence resources and mate availability for plants. Because of different resource/mating demands of the male and female reproductive pathways, environmental variation can drive geographic patterns of sex‐specific factors in sexually polymorphic species. Yet, the relationship between environment and sex, sexual dimorphism or sex chromosomes at the range‐wide scale is underexamined.Using ~7000 herbarium and iNaturalist specimens we generate a landscape‐scale understanding of how sex ratio and sexual dimorphism vary with geographic, climatic and soil gradients in the sexually polymorphic wild strawberry (Fragaria virginiana) and test whether these conform to predictions from theory. Then, for ~300 specimens we use genotyping of the sex‐determining region (SDR haplotypes) to reveal geographic and phenotypic patterns in sex chromosome types.Across North America, the sex ratio was hermaphrodite/male‐biased and was associated more with soil attributes than climate. Sex ratio‐environment associations matched predictions for subdioecy in the West but for gynodioecy in the East. Climatic factors correlated with sexual dimorphism in traits related to carbon acquisition (leaf size and runnering while flowering) but not mate access (petal size, flowering time). Variation in sexual dimorphism was due to one sex being more responsive to the environmental variation than the other. Specifically, leaf length in females was more responsive to variation in precipitation than in hermaphrodite/males, but the probability of runnering while flowering in hermaphrodite/males was more responsive to variation in temperature than in females. The ancestral sex chromosome type was most common overall. But the frequency of the more derived sex chromosomes varied with environmental factors that differed between East–West regions.Synthesis. A landscape‐level perspective revealed that variation in soil and climate factors can explain geospatial variation in sex ratio and sexual dimorphism in a wild strawberry. Variation in sex ratio was associated more with soil resources than climate, while variation in sexual dimorphism was the result of sex‐differential responses to climate for vegetative traits but a similar response to abiotic factors in mate access traits. Finally, sex chromosome types were associated with soil moisture and precipitation in ways that could contribute to the evolution of sex determination. 
    more » « less
  4. Abstract The common bed bug, Cimex lectularius, is a globally distributed pest insect of medical, veterinary, and economic importance. Previous reference genome assemblies for this species were generated from short read sequencing data, resulting in a ~650 Mb composed of thousands of contigs. Here, we present a haplotype-resolved, chromosome-level reference genome, generated from an adult Harlen strain female specimen. Using PacBio long read and Omni-C proximity sequencing, we generated a 540 Mb genome with 15 chromosomes (13 autosomes and 2 sex chromosomes - X1X2) with an N50 > 30 Mb and BUSCO > 90%. Previous karyotyping efforts indicate an XY sex chromosome system, with 2n=26 and X1X1X2X2 females and X1X2Y males; however significant fragmentation of the X chromosome has also been reported. We further use whole genome resequencing data from males and females to identify the X1 and X2 chromosomes based on sex biases in coverage. This highly contiguous reference genome assembly provides a much-improved resource for identifying chromosomal genome architecture, and for interpreting patterns of urban outbreaks and signatures of selection linked to insecticide resistance. 
    more » « less
  5. Mank, Judith (Ed.)
    Abstract African cichlid fishes are known for their high rates of phenotypic evolution. A rapid rate of diversification is apparent also in the diversity of their sex chromosomes. To date, sex determiners have been identified on 18 of 22 chromosomes in the standard karyotype. Here, we use whole-genome sequencing to characterize the sex chromosomes of seven populations of basal haplochromines, focusing on the genus Pseudocrenilabrus. We identify six new sex chromosome systems, including the first report of a cichlid sex–determining system on linkage group 12. We then quantify the rates and patterns of sex chromosome turnover in this clade. Finally, we test whether some autosomes become sex chromosomes in East African cichlids more often than expected by chance. 
    more » « less