Functional Divergence of Multiple Duplicated Foxl2 Homeologs and Alleles in a Recurrent Polyploid Fish

Abstract

Evolutionary fates of duplicated genes have been widely investigated in many polyploid plants and animals, but research is scarce in recurrent polyploids. In this study, we focused on foxl2, a central player in ovary, and elaborated the functional divergence in gibel carp (Carassius gibelio), a recurrent auto-allo-hexaploid fish. First, we identified three divergent foxl2 homeologs (Cgfoxl2a-B, Cgfoxl2b-A, and Cgfoxl2b-B), each of them possessing three highly conserved alleles and revealed their biased retention/loss. Then, their abundant sexual dimorphism and biased expression were uncovered in hypothalamic–pituitary–gonadal axis. Significantly, granulosa cells and three subpopulations of thecal cells were distinguished by cellular localization of CgFoxl2a and CgFoxl2b, and the functional roles and the involved process were traced in folliculogenesis. Finally, we successfully edited multiple foxl2 homeologs and/or alleles by using CRISPR/Cas9. Cgfoxl2a-B deficiency led to ovary development arrest or complete sex reversal, whereas complete disruption of Cgfoxl2b-A and Cgfoxl2b-B resulted in the depletion of germ cells. Taken together, the detailed cellular localization and functional differences indicate that Cgfoxl2a and Cgfoxl2b have subfunctionalized and cooperated to regulate folliculogenesis and gonad differentiation, and Cgfoxl2b has evolved a new function in oogenesis. Therefore, the current study provides a typical case of homeolog/allele diversification, retention/loss, biased expression, and sub-/neofunctionalization in the evolution of duplicated genes driven by polyploidy and subsequent diploidization from the recurrent polyploid fish.

Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish

“…In this study, we identified two homeologs of Cgviperins with about 91% identity, and each homeolog has three alleles with high identities (≥99.0%) and located on three homologous chromosomes separately (Supplementary Figure S1 and Figure 1C). Compared to zebrafish, our results (Figures 1B, D) indicated that the duplication of Cgviperin, same as gibel carp other genes (i.e., dmrt1, foxl2, nanos2 and bmp15) (55,60,69,70), may derive from the early allotetraploidy (4R) and a late autotriploidy (5R) event. In addition, Cgviperin-A and Cgviperin-B showed a different tissue-dependent constitutive expressions, suggesting A or B homologs might occur dominant or biased expression of homeologs during gibel carp evolution.…”

“…One of the two duplicates may be fractionated (deleted), or both may be retained, or diverge and evolve (sub- or neofunctionalization) ( 3 ). Recently, we revealed the biased expression and sub-/neofunctionalization of multiple duplicated foxl2 homeologs and alleles in gibel carp ( 60 ). Innate immunity plays a vital role in the first barrier protecting the host from invading viruses ( 68 ).…”

“…Then, Cgviperin-A -BAC-DNA and Cgviperin-B -BAC-DNA were labeled by Biotin-Nick Translation Mix (Roche) and DIG-Nick Translation Mix, respectively. Chromosome preparation and FISH analyses were performed as described previously ( 55 , 60 ). All metaphase chromosomes were counterstained with 4’, 6-diamidino-2-phenylindole (DAPI).…”

Genotypic Males Play an Important Role in the Creation of Genetic Diversity in Gynogenetic Gibel Carp

“…Hexaploid gibel carp (C. gibelio) was originated from sympatric progenitor tetraploid crucian carp (Carassius auratus) via autotriploidy about 0.5 million years ago (Mya) (Li et al, 2014). Genomic anatomy and single-gene analysis revealed that gibel carp was an allohexaploid (AAABBB) in comparison with the allotetraploid crucian carp (AABB) (Li et al, 2014;Gan et al, 2021;Yu et al, 2021;Wang et al, under review). Three alleles in subgenome A and three alleles in subgenome B make the genome unable to pair during meiosis (Gan et al, 2021) and the hexaploid gibel carp conquers the reproductive obstacles via unisexual gynogenesis (Gui and Zhou, 2010;Zhou and Gui, 2017), in which unreduced eggs are activated by the sperm of sympatric sexual species to initiate embryogenesis with only maternal genetic information.…”

“…Genomic anatomy and single-gene analysis revealed that gibel carp was an allohexaploid (AAABBB) in comparison with the allotetraploid crucian carp (AABB) (Li et al, 2014;Gan et al, 2021;Yu et al, 2021;Wang et al, under review). Three alleles in subgenome A and three alleles in subgenome B make the genome unable to pair during meiosis (Gan et al, 2021) and the hexaploid gibel carp conquers the reproductive obstacles via unisexual gynogenesis (Gui and Zhou, 2010;Zhou and Gui, 2017), in which unreduced eggs are activated by the sperm of sympatric sexual species to initiate embryogenesis with only maternal genetic information. Compared with sexual tetraploid crucian carp, gynogenetic hexaploid gibel carp exhibits wider geographic distribution and higher genetic diversity (Jiang et al, 2013;Liu et al, 2017a).…”