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Article ; Online: Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry.

Cauret, Caroline M S / Mortimer, Sebastian M E / Roberti, Marcelina C / Ashman, Tia-Lynn / Liston, Aaron

2022 Volume 12, Issue 8

Abstract: When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early ... ...

Abstract	When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.
MeSH term(s)	Biological Evolution ; Chromosomes, Plant/genetics ; DNA Transposable Elements ; Fragaria/genetics ; Sex Chromosomes/genetics
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2022-06-03
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac139
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa.

Premachandra, Tharindu / Cauret, Caroline M S / Conradie, Werner / Measey, John / Evans, Ben J

G3 (Bethesda, Md.)

2022 Volume 13, Issue 2

Abstract: Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may ... ...

Abstract	Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa.
MeSH term(s)	Animals ; Xenopus laevis/genetics ; Metagenomics ; Genome ; Genomics ; Africa, Southern ; Evolution, Molecular ; Phylogeny
Language	English
Publishing date	2022-12-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac325
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Article ; Online: Functional dissection and assembly of a small, newly evolved, W chromosome-specific genomic region of the African clawed frog Xenopus laevis.

Cauret, Caroline M S / Jordan, Danielle C / Kukoly, Lindsey M / Burton, Sarah R / Anele, Emmanuela U / Kwiecien, Jacek M / Gansauge, Marie-Theres / Senthillmohan, Sinthu / Greenbaum, Eli / Meyer, Matthias / Horb, Marko E / Evans, Ben J

PLoS genetics

2023 Volume 19, Issue 10, Page(s) e1010990

Abstract: Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small W chromosome- ... ...

Abstract	Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small W chromosome-specific region of the frog Xenopus laevis that contains only three genes (dm-w, scan-w, ccdc69-w) and that drives female differentiation. Using gene editing, we found that the sex-determining function of this region requires dm-w but that scan-w and ccdc69-w are not essential for viability, female development, or fertility. Analysis of mesonephros+gonad transcriptomes during sexual differentiation illustrates masculinization of the dm-w knockout transcriptome, and identifies mostly non-overlapping sets of differentially expressed genes in separate knockout lines for each of these three W-specific gene compared to wildtype sisters. Capture sequencing of almost all Xenopus species and PCR surveys indicate that the female-determining function of dm-w is present in only a subset of species that carry this gene. These findings map out a dynamic evolutionary history of a newly evolved W chromosome-specific genomic region, whose components have distinctive functions that frequently degraded during Xenopus diversification, and evidence the evolutionary consequences of recombination suppression.
MeSH term(s)	Animals ; Male ; Female ; Xenopus laevis/metabolism ; Transcription Factors/genetics ; Sex Determination Processes/genetics ; Genomics ; Chromosomes/genetics ; Chromosomes/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2023-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1010990
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Article ; Online: (with research data) Limited genomic consequences of hybridization between two African clawed frogs, Xenopus gilli and X. laevis (Anura: Pipidae).

Furman, Benjamin L S / Cauret, Caroline M S / Colby, Graham A / Measey, G John / Evans, Ben J

Scientific reports

2017 Volume 7, Issue 1, Page(s) 1091

Abstract: The Cape platanna, Xenopus gilli, an endangered frog, hybridizes with the African clawed frog, X. laevis, in South Africa. Estimates of the extent of gene flow between these species range from pervasive to rare. Efforts have been made in the last 30 ... ...

Abstract	The Cape platanna, Xenopus gilli, an endangered frog, hybridizes with the African clawed frog, X. laevis, in South Africa. Estimates of the extent of gene flow between these species range from pervasive to rare. Efforts have been made in the last 30 years to minimize hybridization between these two species in the west population of X. gilli, but not the east populations. To further explore the impact of hybridization and the efforts to minimize it, we examined molecular variation in one mitochondrial and 13 nuclear genes in genetic samples collected recently (2013) and also over two decades ago (1994). Despite the presence of F
MeSH term(s)	Animals ; Chimera/genetics ; Gene Flow ; Genetic Variation ; Genomics ; South Africa ; Xenopus/genetics
Language	English
Publishing date	2017-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-01104-9
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Article ; Online: Sex chromosome degeneration, turnover, and sex-biased expression of sex-linked transcripts in African clawed frogs (

Song, Xue-Ying / Furman, Benjamin L S / Premachandra, Tharindu / Knytl, Martin / Cauret, Caroline M S / Wasonga, Domnick Victor / Measey, John / Dworkin, Ian / Evans, Ben J

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2021 Volume 376, Issue 1832, Page(s) 20200095

Abstract: The tempo of sex chromosome evolution-how quickly, in what order, why and how their particular characteristics emerge during evolution-remains poorly understood. To understand this further, we studied three closely related species of African clawed frog ( ...

Abstract	The tempo of sex chromosome evolution-how quickly, in what order, why and how their particular characteristics emerge during evolution-remains poorly understood. To understand this further, we studied three closely related species of African clawed frog (genus
MeSH term(s)	Animals ; Female ; Male ; Sex Characteristics ; Sex Chromosomes/genetics ; Sex Determination Processes ; Transcription, Genetic ; Xenopus/genetics
Language	English
Publishing date	2021-07-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2020.0095
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Article ; Online: A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome.

Furman, Benjamin L S / Cauret, Caroline M S / Knytl, Martin / Song, Xue-Ying / Premachandra, Tharindu / Ofori-Boateng, Caleb / Jordan, Danielle C / Horb, Marko E / Evans, Ben J

PLoS genetics

2020 Volume 16, Issue 11, Page(s) e1009121

Abstract: In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among-and ... ...

Abstract	In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among-and even within-species. To understand these systems more, we investigated a rare example of a frog with three sex chromosomes: the Western clawed frog, Xenopus tropicalis. We demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a very similar genomic location as a previously known female-determining factor on the W chromosome. Nucleotide polymorphism of expressed transcripts suggests genetic degeneration on the W chromosome, emergence of a new Y chromosome from an ancestral Z chromosome, and natural co-mingling of the W, Z, and Y chromosomes in the same population. Compared to the rest of the genome, a small sex-associated portion of the sex chromosomes has a 50-fold enrichment of transcripts with male-biased expression during early gonadal differentiation. Additionally, X. tropicalis has sex-differences in the rates and genomic locations of recombination events during gametogenesis that are similar to at least two other Xenopus species, which suggests that sex differences in recombination are genus-wide. These findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes, demonstrate that several characteristics of old and established sex chromosomes (e.g., nucleotide divergence, sex biased expression) can arise well before sex chromosomes become cytogenetically distinguished, and show how these characteristics can have lingering consequences that are carried forward through sex chromosome turnovers.
MeSH term(s)	Animals ; Female ; Genetic Fitness ; Ghana ; Male ; Recombination, Genetic ; Sex Chromosomes/genetics ; Sex Determination Processes/genetics ; Sex Differentiation/genetics ; Xenopus/genetics
Language	English
Publishing date	2020-11-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1009121
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Article ; Online: Erratum to: Developmental systems drift and the drivers of sex chromosome evolution.

Cauret, Caroline M S / Gansauge, Marie-Theres / Tupper, Andrew S / Furman, Benjamin L S / Knytl, Martin / Song, Xue / Greenbaum, Eli / Meyer, Matthias / Evans, Ben J

Molecular biology and evolution

2020 Volume 37, Issue 6, Page(s) 1844

Language	English
Publishing date	2020-01-30
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msz286
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Article ; Online: Xenopus fraseri: Mr. Fraser, where did your frog come from?

Evans, Ben J / Gansauge, Marie-Theres / Stanley, Edward L / Furman, Benjamin L S / Cauret, Caroline M S / Ofori-Boateng, Caleb / Gvoždík, Václav / Streicher, Jeffrey W / Greenbaum, Eli / Tinsley, Richard C / Meyer, Matthias / Blackburn, David C

PloS one

2019 Volume 14, Issue 9, Page(s) e0220892

Abstract: A comprehensive, accurate, and revisable alpha taxonomy is crucial for biodiversity studies, but is challenging when data from reference specimens are difficult to collect or observe. However, recent technological advances can overcome some of these ... ...

Abstract	A comprehensive, accurate, and revisable alpha taxonomy is crucial for biodiversity studies, but is challenging when data from reference specimens are difficult to collect or observe. However, recent technological advances can overcome some of these challenges. To illustrate this, we used modern approaches to tackle a centuries-old taxonomic enigma presented by Fraser's Clawed Frog, Xenopus fraseri, including whether X. fraseri is different from other species, and if so, where it is situated geographically and phylogenetically. To facilitate these inferences, we used high-resolution techniques to examine morphological variation, and we generated and analyzed complete mitochondrial genome sequences from all Xenopus species, including >150-year-old type specimens. Our results demonstrate that X. fraseri is indeed distinct from other species, firmly place this species within a phylogenetic context, and identify its minimal geographic distribution in northern Ghana and northern Cameroon. These data also permit novel phylogenetic resolution into this intensively studied and biomedically important group. Xenopus fraseri was formerly thought to be a rainforest endemic placed alongside species in the amieti species group; in fact this species occurs in arid habitat on the borderlands of the Sahel, and is the smallest member of the muelleri species group. This study illustrates that the taxonomic enigma of Fraser's frog was a combined consequence of sparse collection records, interspecies conservation and intraspecific polymorphism in external anatomy, and type specimens with unusual morphology.
MeSH term(s)	Animals ; Biodiversity ; Conserved Sequence ; DNA Barcoding, Taxonomic ; Evolution, Molecular ; Genome, Mitochondrial ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Models, Anatomic ; Phylogeny ; X-Ray Microtomography ; Xenopus/anatomy & histology ; Xenopus/classification
Language	English
Publishing date	2019-09-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0220892
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Article ; Online: Developmental Systems Drift and the Drivers of Sex Chromosome Evolution.

Cauret, Caroline M S / Gansauge, Marie-Theres / Tupper, Andrew S / Furman, Benjamin L S / Knytl, Martin / Song, Xue-Ying / Greenbaum, Eli / Meyer, Matthias / Evans, Ben J

Molecular biology and evolution

2019 Volume 37, Issue 3, Page(s) 799–810

Abstract: Phenotypic invariance-the outcome of purifying selection-is a hallmark of biological importance. However, invariant phenotypes might be controlled by diverged genetic systems in different species. Here, we explore how an important and invariant phenotype- ...

Abstract	Phenotypic invariance-the outcome of purifying selection-is a hallmark of biological importance. However, invariant phenotypes might be controlled by diverged genetic systems in different species. Here, we explore how an important and invariant phenotype-the development of sexually differentiated individuals-is controlled in over two dozen species in the frog family Pipidae. We uncovered evidence in different species for 1) an ancestral W chromosome that is not found in many females and is found in some males, 2) independent losses and 3) autosomal segregation of this W chromosome, 4) changes in male versus female heterogamy, and 5) substantial variation among species in recombination suppression on sex chromosomes. We further provide evidence of, and evolutionary context for, the origins of at least seven distinct systems for regulating sex determination among three closely related genera. These systems are distinct in their genomic locations, evolutionary origins, and/or male versus female heterogamy. Our findings demonstrate that the developmental control of sexual differentiation changed via loss, sidelining, and empowerment of a mechanistically influential gene, and offer insights into novel factors that impinge on the diverse evolutionary fates of sex chromosomes.
MeSH term(s)	Animals ; Biological Evolution ; Evolution, Molecular ; Female ; Genetic Drift ; Male ; Phenotype ; Pipidae/genetics ; Pipidae/physiology ; Recombination, Genetic ; Selection, Genetic ; Sex Chromosomes/genetics ; Sex Determination Processes ; Sex Differentiation
Language	English
Publishing date	2019-11-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msz268
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