Analysis of Sry duplications on the Rattus norvegicus Y-chromosome

Prokop, Jeremy W.; Underwood, Adam; Turner, Monte E.; Miller, N.G.A.; Pietrzak, Dawn; Scott, Sarah E.; Smith, Chris; Milsted, Amy

doi:10.1186/1471-2164-14-792

Cited by 20 publications

(28 citation statements)

References 38 publications

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“…One encompasses the two copies of the male-determining gene SRY. Multiple SRY copies are found in dog (Li et al 2013a) and some rodent species (e.g., Lundrigan and Tucker 1997;Murata et al 2010;Prokop et al 2013), but there has previously been no suggestion of this being the case in the pig. While most other species with multiple SRY copies have identifiable sequence differences between the copies in a single individual, there is also a known example in rabbits of a palindrome encompassing SRY, with gene conversion maintaining sequence identity (Geraldes et al 2010).…”

Section: Palindromic Sequencesmentioning

confidence: 98%

The pig X and Y Chromosomes: structure, sequence, and evolution

et al. 2015

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We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes-both single copy and amplified-on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

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Section: Palindromic Sequencesmentioning

confidence: 98%

The pig X and Y Chromosomes: structure, sequence, and evolution

et al. 2015

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“…Despite locating flanking sequences from 18 species, only 17 were used in our analysis. Sequences from the rat were excluded on the basis of high copy number [ 15 ], and inability to determine which copy(/ies) may be testis-determining. Though the rat has the highest Sry copy number (11) among the species we examined, duplicate copies of Sry are also known to be present in pig and rabbit.…”

Section: Resultsmentioning

confidence: 99%

Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species

Bailey

Koopman

2015

BMC Dev Biol

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BackgroundSex determination in mammals requires expression of the Y-linked gene Sry in the bipotential genital ridges of the XY embryo. Even minor delay of the onset of Sry expression can result in XY sex reversal, highlighting the need for accurate gene regulation during sex determination. However, the location of critical regulatory elements remains unknown. Here, we analysed Sry flanking sequences across many species, using newly available genome sequences and computational tools, to better understand Sry’s genomic context and to identify conserved regions predictive of functional roles.MethodsFlanking sequences from 17 species were analysed using both global and local sequence alignment methods. Multiple motif searches were employed to characterise common motifs in otherwise unconserved sequence.ResultsWe identified position-specific conservation of binding motifs for multiple transcription factor families, including GATA binding factors and Oct/Sox dimers. In contrast with the landscape of extremely low sequence conservation around the Sry coding region, our analysis highlighted a strongly conserved interval of ~106 bp within the Sry promoter (which we term the Sry Proximal Conserved Interval, SPCI). We further report that inverted repeats flanking murine Sry are much larger than previously recognised.ConclusionsThe unusually fast pace of sequence drift on the Y chromosome sharpens the likely functional significance of both the SPCI and the identified binding motifs, providing a basis for future studies of the role(s) of these elements in Sry regulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12861-015-0085-6) contains supplementary material, which is available to authorized users.

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“…Multiple SRY copies are found in dog (Li et al 2013a) and some rodent species (e.g. Prokop et al 2013; Lundrigan and Tucker 1997; Murata et al 2010), but there has previously been no suggestion of this being the case in the pig. Prior sequencing of the SRY gene and comparison across different pig breeds has given no evidence for polymorphisms in the recovered SRY sequence from any individual, despite there being breed-specific differences - i.e.…”

Section: Discussionmentioning

confidence: 98%

The pig X and Y chromosomes: structure, sequence and evolution

Skinner

Sargent

Churcher

et al. 2014

Preprint

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We have generated an improved assembly and gene annotation of the pig X chromosome, and a first draft assembly of the pig Y chromosome, by sequencing BAC and fosmid clones, and incorporating information from optical mapping and fibre-FISH. The X chromosome carries 1,014 annotated genes, 689 of which are protein-coding. Gene order closely matches that found in Primates (including humans) and Carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X chromosome were absent from the pig (e.g. the cancer/testis antigen family) or inactive (e.g. AWAT1), and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y chromosome assembly focussed on two clusters of male-specific low-copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. The long arm of the chromosome is almost entirely repetitive, containing previously characterised sequences. Many of the ancestral X-related genes previously reported in at least one mammalian Y chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes - both single copy and amplified - on the pig Y, to compare the pig X and Y chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y chromosome evolution.

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Analysis of Sry duplications on the Rattus norvegicus Y-chromosome

Cited by 20 publications

References 38 publications

The pig X and Y Chromosomes: structure, sequence, and evolution

The pig X and Y Chromosomes: structure, sequence, and evolution

Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species

The pig X and Y chromosomes: structure, sequence and evolution

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