Evolution of a sex megachromosome

Conte, Matthew A.; Clark, Frances E.; Roberts, Reade B.; Xu, Luohao; Zhou, Qi; Wang, Deshou; Kocher, Thomas D.

doi:10.1101/2020.07.02.182808

Cited by 3 publications

(5 citation statements)

References 118 publications

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“…It is rich in long‐coding RNA, genes related to immune response and regulation, and repetitive elements. It has also been reported as containing a sex‐determination locus in Oreochromis , albeit not in O. niloticus itself (Conte et al., 2020). Collectively, the high genetic diversity of this linkage group explains the relatively low F ST observed between O. urolepis and O. niloticus , and between other species pairs.…”

Section: Discussionmentioning

confidence: 99%

“…On LG3, F ST was lower, but it is notable that this shows an unusually high level of nucleotide (pi) diversity in all our studied Oreochromis populations (Figure ), as well as a high level of absolute sequence divergence ( Dxy ) between all populations (Figure ). Given that LG3 is two to three times larger than any other in the Oreochromis genome (Figure 5; Conte et al., 2019), LG3 has been referred to as a megachromosome, and is likely to have arisen from fusion with an ancestral B‐chromosome (Conte et al., 2020). It is rich in long‐coding RNA, genes related to immune response and regulation, and repetitive elements.…”

Section: Discussionmentioning

confidence: 99%

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Newly discovered cichlid fish biodiversity threatened by hybridization with non‐native species

et al. 2020

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Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013–2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe × niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Newly discovered cichlid fish biodiversity threatened by hybridization with non‐native species

et al. 2020

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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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“…It is rich in long-coding RNA, genes related to immune response and regulation, and repetitive elements. It has also been reported as containing a sex-determination locus in Oreochromis, albeit not in O. niloticus itself (Conte et al 2020). Collectively, the high genetic diversity of this linkage group explains the relatively low FST observed between O. urolepis and O. niloticus, and between other species pairs.…”

Section: Heterogeneity Of Admixture Across the Genomementioning

confidence: 89%

“…On account of this linkage group being 2-3 times larger than any other in the Oreochromis genome ( Fig. 6; Conte et al 2019), LG3 has been referred to as a megachromosome, and is likely to consist of a fusion with an ancestral Bchromosome (Conte et al 2020). It is rich in long-coding RNA, genes related to immune response and regulation, and repetitive elements.…”

Section: Heterogeneity Of Admixture Across the Genomementioning

confidence: 99%

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species

Blackwell

Ford

Ciezarek

et al. 2020

Preprint

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Invasive freshwater fish systems are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically-disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe x niloticus hybrids in three lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged approximately 140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly-discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

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Evolution of a sex megachromosome

Cited by 3 publications

References 118 publications

Newly discovered cichlid fish biodiversity threatened by hybridization with non‐native species

Newly discovered cichlid fish biodiversity threatened by hybridization with non‐native species

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

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species

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