Changing sex for selfish gain: B chromosomes of Lake Malawi cichlid fish

Clark, Frances E.; Köcher, Thomas

doi:10.1038/s41598-019-55774-8

Cited by 39 publications

(42 citation statements)

References 77 publications

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“…Both REs dramatically increased the TE content, and decreased the recombination rate across over two thirds of the LG3 region (Conte et al., 2019), compared to other LGs. The mechanism of these REs still remains unknown, but it was proposed that the fusion between the ancestral LG3 and a highly repetitive B chromosome might account for it (Clark & Kocher, 2019; Conte et al., 2020). The classic model of sex chromosome evolution, as indicated by mammals and birds, hypothesizes that the origination of SD genes would select for suppression of recombination and lead to accumulation of repetitive elements on the Y or W chromosomes (Charlesworth et al., 2005).…”

Section: Discussionmentioning

confidence: 99%

High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

Zhao

Zhu

et al. 2020

Molecular Ecology Resources

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Tilapias are one of the most farmed fishes that are coined as “aquatic chicken” by the food industry. Nile tilapia and blue tilapia exhibit very recent transition of sex chromosome systems since their divergence approximately five million years ago, making them a great model for elucidating the molecular and evolutionary mechanisms of sex chromosome turnovers. Studies of their sex‐determining pathways are also critical for developing genetic sex control in aquaculture. We report here the newly produced genomes of Nile tilapia and blue tilapia that integrate long‐read sequencing and chromatin conformation data. The two nearly complete genomes have anchored over 97% of the sequences into linkage groups (LGs), and assembled majorities of complex repetitive regions including telomeres, centromeres and rDNA clusters. In particular, we inferred two episodes of repeat expansion at LG3 respectively in the ancestor of cichlids and that of tilapias. The consequential large heterochromatic region concentrated at one end of LG3 comprises tandem arrays of mRNA and small RNA genes, among which we have identified a candidate female determining gene Paics in blue tilapia. Paics shows female‐specific patterns of single‐nucleotide variants, copy numbers and expression patterns in gonads during early gonadogenesis. Our work provides a very important genomic resource for functional studies of cichlids, and suggested that unequal distribution of repeat content that impacts the local recombination rate might make some chromosomes more likely to become sex chromosomes.

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Section: Discussionmentioning

confidence: 99%

High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

Zhao

Zhu

et al. 2020

Molecular Ecology Resources

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“…Because the B blocks were found in Kpandu males and Koka females, they created strong differentiation between the sexes in each population, but these signals were independent of the true genetic sex-determining locus. It appears unlikely that the putative B chromosomes play a role as a female W sex-determiner such as in some Lake Malawi cichlids [ 27 ]. However, we are not able to determine the frequency of this B chromosome in our wild populations since we pooled the individual DNAs prior to sequencing.…”

Section: Discussionmentioning

confidence: 99%

“…A complex scenario has been found for various populations of Astatotilapia burtoni , including an XYW system mapped to LG13, an XY system on LG18 and an XY system on a fusion comprising LG5 and LG14 [ 24 , 25 ]. In addition, some species from Lake Malawi possess female-specific B chromosomes that carry a female sex determiner, that is epistatically dominant to the LG7 XY system [ 26 , 27 ].…”

Section: Introductionmentioning

confidence: 99%

Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia

Triay

Conte

Baroiller

et al. 2020

Genes

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In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.

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“…Many Lake Malawi cichlid species harbor a B chromosome that is present as a single copy and only in females. This B chromosome carries an epistatically dominant female (W) sex-determiner, which likely evolved to promote the transmission of the B chromosome through female meiosis (Clark et al 2017;Clark and Kocher 2019). In Lake Victoria cichlids, a different B chromosome persists in high frequency (85% of individuals in all species examined).…”

Section: Introductionmentioning

confidence: 99%

“…Either the autosome or the B chromosome could have been carrying a sex-determination locus prior to fusion. The B chromosome may have carried a sexdetermination locus to favor its transmission through meiotic drive (Clark and Kocher 2019). Such a fusion might be favored if it associated sexually antagonistic variation with the sex determiner, or if it contributed to the drive of the B chromosome.…”

Section: Introductionmentioning

confidence: 99%

Evolution of a sex megachromosome

Conte

Clark

Roberts

et al. 2020

Preprint

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AbstractChromosome size and morphology vary within and among species, but little is known about either the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual megachromosome that is ~3 times longer than any of the other chromosomes. This megachromosome functions as a sex chromosome in some of these species. We explore two hypotheses of how this sex megachromosome may have evolved. The first hypothesis proposes that it developed by the accumulation of repetitive elements as recombination was reduced around a dominant sex-determination locus, as suggested by traditional models of sex chromosome evolution. An alternative hypothesis is that the megachromosome originated via the fusion of an autosome with a highly-repetitive B chromosome, one of which had carried a sex-determination locus. Here we test these hypotheses using comparative analysis of several chromosome-scale cichlid and teleost genomes. We find the megachromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. A WZ sex-determination locus encompasses the last ~105Mbp of the 134Mbp megachromosome and the last 47Mbp of the megachromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal the megachromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long non-coding RNAs. Although the origin of this megachromosome remains ambiguous, it has clearly been a focal point of extensive evolutionary genomic conflicts. This megachromosome represents an interesting system for studying sex chromosome evolution and genomic conflicts.

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Changing sex for selfish gain: B chromosomes of Lake Malawi cichlid fish

Cited by 39 publications

References 77 publications

High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia

Evolution of a sex megachromosome

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