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Fulltext Turnovers of Sex-Determining Mutation in the Golden Pompano and Related Species Provide Insights into Microevolution of Undifferentiated Sex Chromosome

Guo L, Malara D, Battaglia P, Waiho K, Davis DA, Deng Y, et al.

Genome Biol Evol, 2024 Mar 02;16(3).
PMID: 38408866 DOI: 10.1093/gbe/evae037

The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.

Matched MeSH terms: Sex Chromosomes/genetics
Presumptive X monosomy in black rats from Malaya

Hoi-Sen Y

Nature, 1971 Aug 13;232(5311):484-5.
PMID: 4937212
Matched MeSH terms: Sex Chromosomes*
A female Norway rat, Rattus norvegicus, with X0 sex chromosome constitution

Yong HS, Dhaliwal SS, Teh KL

Naturwissenschaften, 1989 Aug;76(8):387-8.
PMID: 2779669
Matched MeSH terms: Sex Chromosomes*
Fulltext Sex Chromosome Turnover in Bent-Toed Geckos (Cyrtodactylus)

Keating SE, Blumer M, Grismer LL, Lin A, Nielsen SV, Thura MK, et al.

Genes (Basel), 2021 01 19;12(1).
PMID: 33477871 DOI: 10.3390/genes12010116

Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed geckos. We uncovered XX/XY sex chromosomes in Cyrtodactylus chaunghanakwaensis and ZZ/ZW sex chromosomes in Cyrtodactylus pharbaungensis. This is the third instance of intrageneric turnover of sex chromosomes in geckos. Additionally, Cyrtodactylus are closely related to another genus with intrageneric turnover, Hemidactylus. Together, these data suggest that sex chromosome turnover may be common in this clade, setting them apart as exceptionally diverse in a group already known for diverse sex determination systems.

Matched MeSH terms: Sex Chromosomes/genetics*
Xga blood group in Chinese, Malays and Indians in Singapore

Saha N, Banerjee B

Vox Sang, 1973;24(6):542-4.
PMID: 4722836
Matched MeSH terms: Sex Chromosomes*
Fulltext Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

Robledo-Ruiz DA, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, et al.

Gigascience, 2022 Mar 29;11.
PMID: 35348671 DOI: 10.1093/gigascience/giac025

BACKGROUND: The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required.
RESULTS: We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene.
CONCLUSIONS: The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.

Matched MeSH terms: Sex Chromosomes
Cytogenetics of ticks (Acari: Ixodoidea). 14. Chromosomes of nine species of Asian haemaphysalines

Oliver JH, Tanaka K, Sawada M

Chromosoma, 1974 May 10;45(4):445-56.
PMID: 4837734
Matched MeSH terms: Sex Chromosomes
Timeframes of speciation, reticulation, and hybridization in the bulldog bat explained through phylogenetic analyses of all genetic transmission elements

Khan FA, Phillips CD, Baker RJ

Syst Biol, 2014 Jan 1;63(1):96-110.
PMID: 24149076 DOI: 10.1093/sysbio/syt062

Phylogenetic comparisons of the different mammalian genetic transmission elements (mtDNA, X-, Y-, and autosomal DNA) is a powerful approach for understanding the process of speciation in nature. Through such comparisons the unique inheritance pathways of each genetic element and gender-biased processes can link genomic structure to the evolutionary process, especially among lineages which have recently diversified, in which genetic isolation may be incomplete. Bulldog bats of the genus Noctilio are an exemplar lineage, being a young clade, widely distributed, and exhibiting unique feeding ecologies. In addition, currently recognized species are paraphyletic with respect to the mtDNA gene tree and contain morphologically identifiable clades that exhibit mtDNA divergences as great as among many species. To test taxonomic hypotheses and understand the contribution of hybridization to the extant distribution of genetic diversity in Noctilio, we used phylogenetic, coalescent stochastic modeling, and divergence time estimates using sequence data from cytochrome-b, cytochrome c oxidase-I, zinc finger Y, and zinc finger X, as well as evolutionary reconstructions based on amplified fragment length polymorphisms (AFLPs) data. No evidence of ongoing hybridization between the two currently recognized species was identified. However, signatures of an ancient mtDNA capture were recovered in which an mtDNA lineage of one species was captured early in the noctilionid radiation. Among subspecific mtDNA clades, which were generally coincident with morphology and statistically definable as species, signatures of ongoing hybridization were observed in sex chromosome sequences and AFLP. Divergence dating of genetic elements corroborates the diversification of extant Noctilio beginning about 3 Ma, with ongoing hybridization between mitochondrial lineages separated by 2.5 myr. The timeframe of species' divergence within Noctilio supports the hypothesis that shifts in the dietary strategies of gleaning insects (N. albiventris) or fish (N. leporinus) are among the most rapid instances of dietary evolution observed in mammals. This study illustrates the complex evolutionary dynamics shaping gene pools in nature, how comparisons of genetic elements can serve for understanding species boundaries, and the complex considerations for accurate taxonomic assignment.

Matched MeSH terms: Sex Chromosomes/genetics
Fulltext Non-invasive sex identification of the white-bellied sea eagle (Haliaeetus leucogaster) through genetic analysis of feathers

Naim DM, Nor SA, Baharuddin MH

Genet. Mol. Res., 2011;10(4):2505-10.
PMID: 22009862 DOI: 10.4238/2011.October.13.7

The white-bellied sea eagle, Haliaeetus leucogaster, displays reversed sexual size dimorphism and is monomorphic for adult plumage coloration. Early attempts to identify sex in sexually monomorphic birds were based on morphological or chromosomal characters, but since avian W-specific DNA sequences were identified, PCR amplification has become commonly used for molecular sexing. We used a PCR test employing primers that amplify two homologous fragments of both the CHD-W gene, unique to females, and the CHD-Z gene, occurring in both sexes. This test was applied to five individuals of H. leucogaster from the Malacca Zoo and to male and female domestic chickens, Gallus domesticus, for comparison. All individuals were sexed successfully with high reproducibility. We conclude that this PCR-based test with feathers as the DNA source is a reliable sexing method for H. leucogaster. This sexing technique is objective and non-invasive and could be used to test sex ratio theories, as well as to help improve conservation and management actions for captive breeding program of this species in Malaysia.

Matched MeSH terms: Sex Chromosomes/genetics*
Fulltext Towards complete and error-free genome assemblies of all vertebrate species

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al.

Nature, 2021 Apr;592(7856):737-746.
PMID: 33911273 DOI: 10.1038/s41586-021-03451-0

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Matched MeSH terms: Sex Chromosomes/genetics
A novel molecular and chromosomal lineage of the anthropophilic Simulium (Simulium) rufibasis subgroup (Diptera: Simuliidae) in Taiwan

Low VL, Takaoka H, Adler PH, Tan TK, Weng FC, Chen CY, et al.

Parasitol Res, 2018 Oct;117(10):3137-3143.
PMID: 30006809 DOI: 10.1007/s00436-018-6011-7

The Simulium rufibasis subgroup is one of three subgroups of the Simulium (Simulium) tuberosum species-group; it is characterized by a pair of clustered stout hairs on the ventral surface of female abdominal segment 7. A member of the S. rufibasis subgroup in Taiwan was investigated morphologically and genetically using the universal cytochrome c oxidase subunit I (COI) barcoding gene and polytene chromosomal banding pattern. The Taiwanese material is morphologically similar to S. rosliramlii Takaoka & Chen from Vietnam and represents the second species of the S. rufibasis subgroup known from Taiwan. It also represents a novel molecular lineage that is distinct from three other primary lineages identified as S. doipuiense, S. doipuiense/S. rufibasis, and S. weji previously reported from Thailand. The mitochondrial evidence for a distinct lineage in Taiwan is supported by chromosomal analysis, which revealed unique sex chromosomes. For nomenclatural stability, we associate the name S. arisanum Shiraki with the Taiwanese entity. Originally described from females from Taiwan, S. arisanum until now has remained an enigmatic species.

Matched MeSH terms: Sex Chromosomes
Chromosomal evolution in the lizard genus Varanus (reptilia)

King M, King D

Aust. J. Biol. Sci., 1975 Feb;28(1):89-108.
PMID: 1164258

The karyotypes have been determined of 16 of the 32 species of the genus Varanus, including animals from Africa, Israel, Malaya and Australia. A constant chromosome number of 2n = 40 was observed. The karyotype is divided into eight pairs of large chromosomes and 12 paris of microchromosomes. A series of chromosomal rearrangements have become established in both size groups of the karyotype and are restricted to centromers shifts, probably caused by pericentric inversion. Species could be placed in one of six distinct karyotype groups which are differentiated by these rearrangements and whose grouping does not always correspond with the current taxonomy. An unusual sex chromosome system of the ZZ/ZW type was present in a number of the species examined. The evolutionary significance of these chromosomal rearrangements, their origin and their mode of establishment are discussed and related to the current taxonomic groupings. The most likely phylogenetic model based on chromosome morphology, fossil evidence and the current distribution of the genus Varanus is presented.

Matched MeSH terms: Sex Chromosomes
Fulltext Genes and genealogy of the guppy fish, Poecilia reticulata

Khoo, Gideon, Lim, Tit Meng, Phang, Violet Pan Eng

Buletin Persatuan Genetik Malaysia, 2006;12(1):5-7.
MyJurnal

Since the early 1950’s, Singapore is internationally known as the guppy-breeding centre. At least 40 different colour varieties of guppies are cultured in Singapore, with each farm specialising in 10 to 15 varieties. These fancy varieties have been developed by skilful farmers through intensive and continual selective breeding. Genes controlling background body pigmentation such as albino (a), blond (b), gold (g) and blue (r) are autosomally inherited and recessive to their wild-type alleles which produce drab olive-brown background coloration. Colour patterns which are superimposed onto wild-type background coloration are due to genes located on the sex chromosomes. These
sex-linked colour genes are dominant and sex-limited to males as their expression requires male hormones. Y-linked colour pattern genes carried by males are inherited only along the paternal line while X-linked genes are present in both sexes. Among the guppy varieties produced locally, only two Y-linked genes, Ssb and Sst, that control snakeskin tail and body patterns, respectively, have been found in varieties with snakeskin-like reticulations. Single colour genes that are both X- and Y-linked produce red (Rdt), blue (Blt), green (Grt), black (Bt) and variegated (Var) patterns
on the caudal fin. The black caudal-peduncle of the Tuxedo variety is the result of Bcp, a gene that is both X- and Ylinked. Different combinations of colour pattern genes and background pigmentation genes as well as interactions among them give rise to various colour phenotypes. For
instance, the inclusion of Bcp in Snakeskin varieties causes black reticulations on the tail fin to be replaced by large, coarse black spots. Neon coloration is produced by interactions between the Ln (light turquoise) gene with Blt, Rdt and Bcp.

Matched MeSH terms: Sex Chromosomes
Fulltext Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

Shi X, Waiho K, Li X, Ikhwanuddin M, Miao G, Lin F, et al.

BMC Genomics, 2018 Dec 29;19(1):981.
PMID: 30594128 DOI: 10.1186/s12864-018-5380-8

BACKGROUND: Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals.
RESULTS: Restriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively.
CONCLUSIONS: Sex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.

Matched MeSH terms: Sex Chromosomes

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