Chromosome-level genome and the identification of sex chromosomes in <i>Uloborus diversus</i>

Miller, Jernelle; Zimin, Aleksey V.; Gordus, Andrew

doi:10.1093/gigascience/giad002

Cited by 12 publications

(3 citation statements)

References 195 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…6 and supplementary fig. S4A, Supplementary Material online) ( Sheffer et al 2021 ; Zhu et al 2022 ; Miller et al 2023 ). Interestingly, Hox cluster B and NK cluster B are both found on the same sex chromosome in H. graminicola (12) and D. silvatica (X), but on separate sex chromosomes in other entelegynes, whereas Hox cluster A is located on an autosome ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Aase-Remedios,

Janssen,

Leite

et al. 2023

Molecular Biology and Evolution

View full text Add to dashboard Cite

Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.

show abstract

Section: Resultsmentioning

confidence: 99%

Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Aase-Remedios,

Janssen,

Leite

et al. 2023

Molecular Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…Sex chromosomes have been identified in multiple spider species (Sheffer et al 2021;Zhu et al 2022;Miller et al 2023), which are denoted with an 'X' in Figure 6. Interestingly, Hox cluster B and NK cluster B are both found on the same sex chromosome in H. graminicola (12) and D. silvatica (X), but on separate sex chromosomes in other entelegynes, whereas Hox cluster A is located on an autosome (Figure 6).…”

Section: Conserved Macrosynteny Of Spider Genomesmentioning

confidence: 99%

Evolution of the spider homeobox gene repertoire by tandem and whole genome duplication

Aase-Remedios

Janßen

Leite

et al. 2023

Preprint

View full text Add to dashboard Cite

Whole genome duplication (WGD) generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. After WGD, retained ohnologues can undergo subfunctionalisation to partition ancestral functions and/or neofunctionalisation, where one copy assumes a new function. We previously found that there had been a WGD in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues were produced by WGD versus tandem duplications. Understanding this is key to determining the relative contributions of tandem duplications and WGD to arachnopulmonate genome evolution. Here we characterised the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that the majority of retained duplicate homeobox genes in spiders likely originated from WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE, in all eight species. Consistently, we noticed one degenerated copy of each cluster in terms of gene content and organisation while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalisation between the duplicated NK genes in the spider Parasteatoda tepidariorum to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.

show abstract

“…The research on early sex determination of birds generally uses appearance and behavioral observation ( Shoji et al, 2015 ; Cunningham et al, 2023 ), laparoscopy ( Dogliero et al, 2017 ), laparotomy ( Lukaszewicz et al, 2017 ), cloaca identification ( Denoël, 2017 ), hormone measurement ( Koch et al, 2019 ), and cell scientific analysis ( Miller et al, 2022 ). However, these identification methods are not very effective and are harmful to individual test subjects, time-consuming, and labor-intensive.…”

Section: Introductionmentioning

confidence: 99%

The development rule of feathers and application of hair root tissue in sex identification of Yangzhou geese

Qi,

Xu,

Liu

et al. 2024

Poultry Science

View full text Add to dashboard Cite

Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

Cited by 12 publications

References 195 publications

Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Evolution of the spider homeobox gene repertoire by tandem and whole genome duplication

The development rule of feathers and application of hair root tissue in sex identification of Yangzhou geese

Contact Info

Product

Resources

About