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Teleosts are important models to study sex chromosomes and sex-determining (SD) genes because they present a variety of sex determination systems. Here, we used Nanopore and Hi-C technologies to generate a high-contiguity chromosome-level genome assembly of a YY southern catfish ( Silurus meridionalis ). The assembly is 750.0 Mb long, with contig N50 of 15.96 Mb and scaffold N50 of 27.22 Mb. We also sequenced and assembled an XY male genome with a size of 727.2 Mb and contig N50 of 13.69 Mb. We identified a candidate SD gene through comparisons to our previous assembly of an XX individual. By resequencing male and female pools, we characterized a 2.38 Mb sex-determining region (SDR) on Chr24. Analysis of read coverage and comparison of the X and Y chromosome sequences showed a Y specific insertion (approx. 500 kb) in the SDR which contained a male-specific duplicate of amhr2 (named amhr2y ). amhr2y and amhr2 shared high-nucleotide identity (81.0%) in the coding region but extremely low identity in the promotor and intron regions. The exclusive expression in the male gonadal primordium and loss-of-function inducing male to female sex reversal confirmed the role of amhr2y in male sex determination. Our study provides a new example of amhr2 as the SD gene in fish and sheds light on the convergent evolution of the duplication of AMH/AMHR2 pathway members underlying the evolution of sex determination in different fish lineages.
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Whole‐genome assembly and annotation for the little yellow croaker ( Larimichthys polyactis ) provide insights into the evolution of hermaphroditism and gonochorism
Abstract The evolutionary direction of gonochorism and hermaphroditism is an intriguing mystery to be solved. The special transient hermaphroditic stage makes the little yellow croaker (Larimichthys polyactis) an appealing model for studying hermaphrodite formation. However, the origin and evolutionary relationship between ofL. polyactisandLarimichthys crocea, the most famous commercial fish species in East Asia, remain unclear. Here, we report the sequence of theL. polyactisgenome, which we found is ~706 Mb long (contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and contains 25,233 protein‐coding genes. Phylogenomic analysis suggested thatL. polyactisdiverged from the common ancestor,L. crocea, approximately 25.4 million years ago. Our high‐quality genome assembly enabled comparative genomic analysis, which revealed several within‐chromosome rearrangements and translocations, without major chromosome fission or fusion events between the two species. Thedmrt1gene was identified as the male‐specific gene inL. polyactis. Transcriptome analysis showed that the expression ofdmrt1and its upstream regulatory gene (rnf183) were both sexually dimorphic.Rnf183, unlike its two paraloguesrnf223andrnf225, is only present inLarimichthysandLatesbut not in other teleost species, suggesting that it originated from lineage‐specific duplication or was lost in other teleosts.Phylogenetic analysis shows that the hermaphrodite stage in maleL. polyactismay be explained by the sequence evolution ofdmrt1. Decoding theL. polyactisgenome not only provides insight into the genetic underpinnings of hermaphrodite evolution, but also provides valuable information for enhancing fish aquaculture.
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- Award ID(s):
- 1928770
- PAR ID:
- 10442573
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology Resources
- Volume:
- 23
- Issue:
- 3
- ISSN:
- 1755-098X
- Format(s):
- Medium: X Size: p. 632-658
- Size(s):
- p. 632-658
- Sponsoring Org:
- National Science Foundation
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