Has recombination changed during the recent evolution of the guppy Y chromosome? DOI Creative Commons
Deborah Charlesworth, Suo Qiu,

Jim Gardner

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 24, 2023

Abstract Genome sequencing and genetic mapping of molecular markers has demonstrated Y-linkage across most the guppy ( Poecilia reticulata ) XY chromosome pair. However, they also revealed exchanges with X, consistent classical observations occasional factors controlling visible male-specific phenotypic traits. It remains unclear whether this fish species an extensive sex-determining region without crossing over (whose suppressed recombination could have evolved under selection created by sexually antagonistic effects male coloration factors), or fully Y-linked is very small, perhaps within a single gene. Population genomic data support cytogenetic results indicating that it terminal 5 Mb 26.5 12, just proximal to highly recombining pseudo-autosomal region, PAR1. Using markers, we studied recombination, focusing on Despite assembly errors in small PAR1, our identifies similar PAR boundaries sires from four populations, suggesting their crossover patterns not changed. Our confirmed crossovers male-determining defining second PAR2, much more rarely than The positions suggest factor repetitive near 21 female assembly. A sex-reversed XX had few region’s low rate depends phenotypic, genetic, sex. Thus rare sex changes, and/or males can explain failure detect variants.

Language: Английский

Sex chromosome evolution: hallmarks and question marks DOI Creative Commons
Paul A. Saunders, Aline Muyle

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(11)

Published: Oct. 16, 2024

Abstract Sex chromosomes are widespread in species with separate sexes. They have evolved many times independently and display a truly remarkable diversity. New sequencing technologies methodological developments allowed the field of molecular evolution to explore this diversity large number model nonmodel organisms, broadening our vision on mechanisms involved their evolution. Diverse studies us better capture common evolutionary routes that shape sex chromosomes; however, we still mostly fail explain why so diverse. We review over half century theoretical empirical work chromosome highlight pending questions origins, turnovers, rearrangements, degeneration, dosage compensation, gene content, rates also report recent progress understanding ultimate reasons for chromosomes’ existence.

Language: Английский

Citations

7
High-yield hybrid breeding of Camellia oleifolia based on ISSR molecular markers DOI Creative Commons

Jinjia Zheng,

Haiqi Su,

Shaosheng Pu

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: June 8, 2024

Abstract Background C. Oleifera is among the world’s largest four woody plants known for their edible oil production, yet contribution rate of improved varieties less than 20%. The species traditional breeding lengthy cycle (20–30 years), occupation land resources, high labor cost, and low accuracy efficiency, which can be enhanced by molecular marker-assisted selection. However, lack high-quality markers hinders genetic analysis breeding. Results Through quantitative traits characterization, diversity assessment, association studies, we generated a selection population with wide diversity, identified five excellent high-yield parental combinations associated reliable ISSR markers. Early criteria were determined based on kernel fresh weight cultivated 1-year seedling height, aided identification these 4 Specific assignment selected individuals as paternal maternal parents was made to capitalize unique attributes. Conclusions Our results indicated that markers-assisted effectively shorten, enhance efficiency facilitate development new system oleifera .

Language: Английский

Citations

4
Evolutionary History of thePoecilia pictaSex Chromosomes DOI Creative Commons
Lydia J. M. Fong, Iulia Darolti, David C. H. Metzger

et al.

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(3)

Published: Feb. 18, 2023

The degree of divergence between the sex chromosomes is not always proportional to their age. In poeciliids, four closely related species all exhibit a male heterogametic chromosome system on same linkage group, yet show remarkable diversity in X and Y divergence. Poecilia reticulata P. wingei, remain homomorphic, picta parae have highly degraded chromosome. To test alternative theories about origin chromosomes, we used combination pedigrees RNA-seq data from families conjunction with DNA-seq collected reticulata, parae, picta. Phylogenetic clustering analysis orthologs, identified through segregation patterns, orthologous sequences demonstrates similar time for both chromosomes. We next k-mer identify shared ancestral sequence across species, suggesting single this group. Together, our results provide key insights into evolution poeciliid illustrate that rate often heterogenous, even over relatively short evolutionary frames.

Language: Английский

Citations

8
Evaluating the role of sexual antagonism in the evolution of sex chromosomes: new data from fish DOI Creative Commons

Sophie Smith,

Kevin Hsiung,

Astrid Böhne

et al.

Current Opinion in Genetics & Development, Journal Year: 2023, Volume and Issue: 81, P. 102078 - 102078

Published: June 26, 2023

The recent increase in available molecular and genomic data for diverse taxa helps to shed new light on long-standing theories. Research into sex chromosome evolution has particularly benefited from a growing number of studies fish, motivated by their highly mechanisms determination. Sexual antagonism is regularly cited as an influential force emergence; however, this so far proves difficult demonstrate. In review, we highlight developments the investigation sexual research fish. We find strong emphasis placed study-organism specific features patterns recombination, rather than evidence comprehensive role antagonism. light, discuss alternative models evolution. conclude that fish represents key resource further research, provided attention given species-specific effects while simultaneously integrating comparative across vital understanding proposed models.

Language: Английский

Citations

8
Partial sex linkage and linkage disequilibrium on the guppy sex chromosome DOI
Suo Qiu, Lengxob Yong, Alastair J. Wilson

et al.

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(21), P. 5524 - 5537

Published: Aug. 25, 2022

The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it proposed that complete sex-linkage evolved across about 3 Mb surrounding this fish's sex-determining locus, followed by suppression further 7 23 XY pair, forming younger "evolutionary strata". Sequences genome show is very similar to X chromosome. Knowing which parts are completely nonrecombining, whether there indeed large nonrecombining region, important understanding its evolution. Here, we describe analyses PoolSeq data in samples from within multiple natural populations Trinidad, yielding new results support previous evidence occasional X. We detected recent demographic changes, notably downstream have higher synonymous site diversity than upstream ones other expected signals bottlenecks. associations sequence variants rather divergence under lack recombination. Although infrequent, frequent enough with SNPs can suggest region locus must be located. Diversity elevated physically chromosome, conforming predictions infrequent carries one or more sexually antagonistic polymorphisms. However, no consistently male-specific were found, supporting suggestion any sex-linked may small.

Language: Английский

Citations

11
Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia DOI
Iulia Darolti, Pedro Almeida, Alison E. Wright

et al.

Journal of Evolutionary Biology, Journal Year: 2022, Volume and Issue: 35(12), P. 1646 - 1658

Published: May 4, 2022

Abstract Studies of sex chromosome systems at early stages divergence are key to understanding the initial process and underlying causes recombination suppression. However, identifying signatures in homomorphic chromosomes can be challenging due high levels sequence similarity between X Y. Variations methodological precision data make all difference detecting subtle patterns or missing them entirely. Recent efforts test for X‐Y differentiation guppy have led contradictory results. Here, we apply different analytical methodologies same set accuracy approaches guppy. Our comparative analysis reveals that most substantial source variation results analyses lies reference genome used. Analyses using custom‐made assemblies focal population species successfully recover a signal across approaches. By contrast, distantly related Xiphophorus variable patterns, both evolution structural variations on . Changes mapping filtering parameters additionally introduce noise obscure signal. illustrate how differences alter perceived highlight best practices study nascent chromosomes.

Language: Английский

Citations

10
Validation of machine learning approach for direct mutation rate estimation DOI Creative Commons
Katarzyna Burda, Mateusz Konczal

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(8), P. 1757 - 1771

Published: July 24, 2023

Mutations are the primary source of all genetic variation. Knowledge about their rates is critical for any evolutionary analyses, but a long time, that knowledge has remained elusive and indirectly inferred. In recent years, parent-offspring comparisons have yielded first direct mutation rate estimates. The analyses are, however, challenging due to high false positives no consensus regarding standardized filtering candidate de novo mutations. Here, we validate application machine learning approach such task estimate guppy (Poecilia reticulata), model species in eco-evolutionary studies. We sequenced 4 parents 20 offspring, followed by screening genomes initial large number mutations was hard-filtered remove false-positive results. These results were compared with estimated supervised approach. Both approaches molecular validation similar ML method uniquely identified three mutations, overall required more hands-on curation had higher negatives. methods concordantly showed difference between families. Estimated here among lowest directly vertebrates; previous research also found low other teleost fishes. discuss potential explanations pattern, as well future utility limitations approaches.

Language: Английский

Citations

4
Has recombination changed during the recent evolution of the guppy Y chromosome? DOI
Deborah Charlesworth, Suo Qiu, Roberta Bergero

et al.

Genetics, Journal Year: 2023, Volume and Issue: 226(1)

Published: Nov. 13, 2023

Genome sequencing and genetic mapping of molecular markers have demonstrated nearly complete Y-linkage across much the guppy (Poecilia reticulata) XY chromosome pair. Predominant factors controlling visible male-specific coloration traits also suggested that these polymorphisms are sexually antagonistic (SA). However, occasional exchanges with X detected, recombination patterns appear to differ between natural populations, suggesting ongoing evolution suppression under selection created by partially sex-linked SA polymorphisms. We used directly estimate maps in sires from 4 populations. The very similar, their crossover not recently changed. Our consistent population genomic results showing variants within terminal 5 Mb 26.5 sex chromosome, 12, most clearly associated maleness factor, albeit incompletely. confirmed crossovers proximal male-determining region, defining a second, rarely recombining, pseudo-autosomal PAR2. This fish species may therefore no completely region (MSY) more extensive than factor. positions few events suggest location for factor physically small repetitive region. A sex-reversed XX male had PAR2, this region's low rate depends on phenotypic, genetic, sex. Thus, rare individuals whose phenotypic sexes differ, and/or PAR2 males can explain failure detect fully Y-linked variants.

Language: Английский

Citations

1
Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei DOI Creative Commons
Mohammed Errbii, Ameka Myrie, Dwight E. Robinson

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(11)

Published: Nov. 1, 2024

Abstract The coffee berry borer (CBB) Hypothenemus hampei was first described in Africa 1867 and has spread to all major coffee-producing regions worldwide, including Jamaica. Using long-read sequencing, we produced a new high-quality reference genome (172.7 Mb) for the Jamaican strain of CBB, with 93% assembled into 14 scaffolds. Whole sequencing pooled samples from different populations across Jamaica showed that CBB harbors low levels genetic diversity alongside an excess low-frequency alleles, indicative recent bottleneck. analyses also surge activity transposable elements (TEs), particularly LINE/R1 LTR/Gypsy elements, within populations. Our findings offer insights evolutionary genomics Jamaica, highlighting potential role TEs shaping this important pest species.

Language: Английский

Citations

0
The Development of Genetic Sex Identification Markers and Evidence of a Male Heterogametic Sex Determination System in Red Shiner DOI
Chad N. Teal, D. Katharine Coykendall, Matthew R. Campbell

et al.

North American Journal of Aquaculture, Journal Year: 2022, Volume and Issue: 85(1), P. 74 - 86

Published: Oct. 31, 2022

Abstract The Red Shiner Cyprinella lutrensis is of increasing management interest as an invasive species that negatively impacts many native fishes throughout North America. Trojan sex chromosome (TSC)‐carrying individuals could theoretically control fish populations by skewing the ratio to 100% male. efficacy TSC‐based programs requires understanding a population's determination system, yet such information lacking for Shiner. We used single‐digest restriction site‐associated DNA sequencing discover sex‐linked single‐nucleotide polymorphisms (SNPs), and we conducted series breeding experiments uncover system. All candidate SNPs fit our selection criteria exhibited pattern male heterogamety. developed two sex‐identification (sex‐ID) marker assays, XY_248 XY_170, which showed phenotype–genotype concordance scores 77.00% 84.35%, respectively. These sex‐ID markers relatively high in females (XY_248 = 96.30%; XY_170 98.61%), allowed selective phenotypically feminized genetic males. observed 3:1 : female spawns from males crossed with wild‐type males, indicative heterogametic system (i.e., XY male/XX female). discovery combination markers, increases likelihood developing effective TSC eradication strategy populations.

Language: Английский

Citations

1