The genome of Roselle's flesh fly Sarcophaga ( Helicophagella) rosellei (Böttcher, 1912).

We present a genome assembly from an individual male Sarcophaga rosellei (Roselle's flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 541 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled. The mitochondrial genome has also been assembled and is 19.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,437 protein coding genes.

The genome sequence of the lesser worm flesh fly, Sarcophaga ( Sarcophaga) subvicina (Baranov, 1937).

We present a genome assembly from an individual male Sarcophaga subvicina (the lesser worm flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 71 megabases in span. Most of the assembly (95.91%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,793 protein coding genes.

The genome sequence of Philonthus cognatus (Stephens, 1832) (Coleoptera, Staphylinidae), a rove beetle.

We present a genome assembly from an individual male Philonthus cognatus (a rove beetle; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 1,030.6 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 20.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 29,629 protein coding genes.

The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758).

We present a genome assembly from an individual male Idaea aversata (the Riband Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,165 protein coding genes.

The genome sequence of the bluish flesh fly, Sarcophaga ( Robineauella) caerulescens (Zetterstedt, 1838).

We present a genome assembly from an individual male Sarcophaga caerulescens (the bluish flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 597 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseudomolecules, including the assembled X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 21.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,559 protein coding genes.

A New Chromosome-Assigned Mongolian Gerbil Genome Allows Characterization of Complete Centromeres and a Fully Heterochromatic Chromosome.

Chromosome-scale genome assemblies based on ultralong-read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation in genome features such as heterochromatin, GC content, recombination rate, and gene content. We present here a new chromosome-scale genome of the Mongolian gerbil (Meriones unguiculatus), which includes the complete sequence of all centromeres. Gerbils are thus the one of the first vertebrates to have their centromeres completely sequenced. Gerbil centromeres are composed of four different repeats of length 6, 37, 127, or 1,747 bp, which occur in simple alternating arrays and span 1-6 Mb. Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intraarm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150 kb) repeated sequences. In addition to characterizing centromeres, our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data and highlight novel patterns involved in the evolution of chromosomes.

The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).

We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,717 protein coding genes.

Incubation temperature alters stripe formation and head colouration in American alligator hatchlings and is unaffected by estradiol-induced sex reversal.

Considerations of the impact climate change has on reptiles are typically focused on habitat change or loss, range shifts and skewed sex ratios in species with temperature-dependent sex determination. Here, we show that incubation temperature alters stripe number and head colouration of hatchling American alligators (Alligator mississippiensis). Animals incubated at higher temperatures (33.5°C) had, on average, one more stripe than those at lower temperatures (29.5°C), and also had significantly lighter heads. These patterns were not affected by estradiol-induced sex reversal, suggesting independence from hatchling sex. Therefore, increases in nest temperatures as a result of climate change have the potential to alter pigmentation patterning, which may have implications for offspring fitness.

The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809).

We present a genome assembly from an individual male Eupithecia vulgata (the Common Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 454.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.1 kilobases in length.

The genome sequence of the variegated flesh fly, Sarcophaga variegata (Scopoli, 1763).

We present a genome assembly from an individual male Sarcophaga variegata (the variegated flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 718.5 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 18.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,660 protein coding genes.

The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).

We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.

The genome sequence of the short-fringed mining bee, Andrena dorsata (Kirby, 1802).

We present a genome assembly from an individual female Andrena dorsata (the short-fringed mining bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence is 277.3 megabases in span. Most of the assembly is scaffolded into 3 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.11 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,916 protein coding genes.

The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766).

We present a genome assembly from an individual male Apamea monoglypha (the Dark Arches, Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,963 protein coding genes.

The genome sequence of Ashworth's Rustic, Xestia ashworthii (Doubleday, 1855).

We present a genome assembly from an individual male Xestia ashworthii (Ashworth's Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 726.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length.

The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809).

We present a genome assembly from an individual female Xestia sexstrigata (the Six-striped Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 638.3 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,104 protein coding genes.

Regulation of posterior Hox genes by sex steroids explains vertebral variation in inbred mouse strains.

A series of elegant embryo transfer experiments in the 1950s demonstrated that the uterine environment could alter vertebral patterning in inbred mouse strains. In the intervening decades, attention has tended to focus on the technical achievements involved and neglected the underlying biological question: how can genetically homogenous individuals have a heterogenous number of vertebrae? Here I revisit these experiments and, with the benefit of knowledge of the molecular-level processes of vertebral patterning gained over the intervening decades, suggest a novel hypothesis for homeotic transformation of the last lumbar vertebra to the adjacent sacral type through regulation of Hox genes by sex steroids. Hox genes are involved in both axial patterning and development of male and female reproductive systems and have been shown to be sensitive to sex steroids in vitro and in vivo. Regulation of these genes by sex steroids and resulting alterations to vertebral patterning may hint at a deep evolutionary link between the ribless lumbar region of mammals and the switch from egg-laying to embryo implantation. An appreciation of the impact of sex steroids on Hox genes may explain some puzzling aspects of human disease, and highlights the spine as a neglected target for in utero exposure to endocrine disruptors.

Runaway GC Evolution in Gerbil Genomes.

Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.

Greater Loss of Female Embryos During Human Pregnancy: A Novel Mechanism.

Given an equal sex ratio at conception, the excess of human males at birth can only be explained by greater loss of females during pregnancy. It is proposed that the bias against females during human development is the result of a greater degree of genetic and metabolic "differentness" between female embryos and maternal tissues than for similarly aged males, and that successful implantation and placentation represents a threshold dichotomy, where the acceptance threshold shifts depending on maternal condition, especially stress. Right and left ovaries are not equal, and neither are the eggs and follicular fluid that they produce, and it is further hypothesized that during times of stress, the implantation threshold is shifted sufficiently to favor survival of females, most likely those originating from the right ovary, and that this, rather than simply a greater loss of males, explains at least some of the variability in the human sex ratio at birth.

A high-density genetic map and molecular sex-typing assay for gerbils.

We constructed a high-density genetic map for Mongolian gerbils (Meriones unguiculatus). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a robust map of 1239 cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1140 genomic scaffolds (containing ~ 20% of annotated genes) into a chromosome-level assembly. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is difficult using current visual methods. Accession ID: Meriones unguiculatus: 10047.

When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species.

Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within a single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographical variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasize how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.