Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

Shao, Feng; Ludwig, Arne; Mao, Yang; Liu, Geoffrey; Peng, Zuogang

doi:10.1093/gigascience/giaa092

Cited by 8 publications

(23 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Next, zooming in on the sex chromosomes at increased resolution and to delineate ZW homologous sequences in situ, we designed a G. affinis Z-chromosome specific oligopaint probe from the repeat-masked male G. affinis LG 01 sequence recently published. The male G. affinis LG 01 assembly was previously identified as the Z-chromosome because it aligned with the female G. affinis LG 01, the W-chromosome [ 24 ].…”

Section: Resultsmentioning

confidence: 99%

“…Before characterizing the sequence differentiation between the sex chromosomes in greater detail, we determined the structural orientation of the W-chromosome with respect to the published W-chromosome sequence assembly [ 24 ]. Unfortunately, we could not recover the centromeric region from the genome assembly of Shao et al [ 24 ] because of obvious difficulties to assemble correctly this highly repetitive region of the W-chromosome. The region between 27.5 and 30.5 Mbp is represented in the genome assembly by a long stretch of “Ns” making it impossible to search, for instance, for the typical alpha-satellites.…”

Section: Resultsmentioning

confidence: 99%

“…With 45 Mbp, the W is the largest and also the only bi-armed, submetacentric element of the karyotype. Except for the smallest pair, all other chromosomes were identified as acrocentric, including the Z, which is the largest acrocentric chromosome with 28 Mbp in size [ 20 – 24 ]. The closely related G .…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

Müller

Guiguen

et al. 2023

BMC Biol

View full text Add to dashboard Cite

Background The Western mosquitofish, Gambusia affinis, is a model for sex chromosome organization and evolution of female heterogamety. We previously identified a G. affinis female-specific marker, orthologous to the aminomethyl transferase (amt) gene of the related platyfish (Xiphophorus maculatus). Here, we have analyzed the structure and differentiation of the G. affinis W-chromosome, using a cytogenomics and bioinformatics approach. Results The long arm of the G. affinis W-chromosome (Wq) is highly enriched in dispersed repetitive sequences, but neither heterochromatic nor epigenetically silenced by hypermethylation. In line with this, Wq sequences are highly transcribed, including an active nucleolus organizing region (NOR). Female-specific SNPs and evolutionary young transposable elements were highly enriched and dispersed along the W-chromosome long arm, suggesting constrained recombination. Wq copy number expanded elements also include female-specific transcribed sequences from the amt locus with homology to TE. Collectively, the G. affinis W-chromosome is actively differentiating by sex-specific copy number expansion of transcribed TE-related elements, but not (yet) by extensive sequence divergence or gene decay. Conclusions The G. affinis W-chromosome exhibits characteristic genomic properties of an evolutionary young sex chromosome. Strikingly, the observed sex-specific changes in the genomic landscape are confined to the W long arm, which is separated from the rest of the W-chromosome by a neocentromere acquired during sex chromosome evolution and may thus have become functionally insulated. In contrast, W short arm sequences were apparently shielded from repeat-driven differentiation, retained Z-chromosome like genomic features, and may have preserved pseudo-autosomal properties.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

Müller

Guiguen

et al. 2023

BMC Biol

View full text Add to dashboard Cite

show abstract

“…We constructed a BLAST database from the Gambusia affinis reference genome assembly SWU_Gaff_1.0 (GCA_019740435.1) (Shao et al 2020) and searched the database for all publicly available coding sequence accessions in GenBank for the melanocortin 1 receptor (MC1R) gene in bony fishes (Actinopterygii). Hits fell into one of two regions, one of which had lower identities and shorter matches to the input sequences than the other.…”

Section: Author Contributionsmentioning

confidence: 99%

Disentangling the effects of male-male competition, reproductive investment and social dominance on telomere length

Harrison¹,

Stuart²,

Jennions³

2023

Preprint

View full text Add to dashboard Cite

Energetically costly events can accelerate telomere loss and ageing via oxidative damage. For adult males, increased levels of reproduction and more frequent fighting for access to mates are therefore stressful experiences that should hasten telomere shortening. Testing for these relationships is, however, confounded by potential correlations between social status and reproductive investment. We used a 2 x 2 experimental design to test how long-term winning or losing contests, in combination with variation in reproductive effort, influenced telomere loss and several key life-history traits in the eastern mosquitofish, Gambusia holbrooki. After 9 weeks there were significant differences between winners and losers in their pre-copulatory reproductive investment (i.e., mating effort), but not in their post-copulatory reproductive investment (i.e., ejaculates). Males that were previously able to mate with females (i.e., had greater past reproductive investment) had significantly lower current mating effort, lower body growth, and slower swimming sperm, but only when males were small. These findings suggest that mating costs incurred from both consistent contest experiences and past reproductive effort depend on male body size. Finally, males that had previously been able to mate with a female did not have shorter telomeres than males that were unable to mate, while there was equivocal evidence that winners had shorter telomeres than losers. This intriguing finding hints at the important role social dynamics play in determining relative male investment into reproduction and somatic maintenance.

show abstract

“…Duffy et al., 2015) to test the fundamental tenets of freshwater ecology, while incorporating an unprecedented scope of natural ecological variation. The recent publication of a high‐quality genome for one mosquitofish species ( Gambusia affinis ) increases their potential use as a genetic model in laboratory and field studies (Hoffberg et al., 2018 WM; Shao et al., 2020 WM). Clearly, mosquitofish have provided a foundation of insights into ecology and evolution, but the future holds considerable potential.…”

Section: Mosquitofish As a Model Systemmentioning

confidence: 99%

From southern swamps to cosmopolitan model: Humanity’s unfinished history with mosquitofish

et al. 2021

View full text Add to dashboard Cite

show abstract

Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

Cited by 8 publications

References 67 publications

Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

Disentangling the effects of male-male competition, reproductive investment and social dominance on telomere length

From southern swamps to cosmopolitan model: Humanity’s unfinished history with mosquitofish

Contact Info

Product

Resources

About