Characterization of the prohormone complement in Amphiprion and related fish species integrating genome and transcriptome assemblies

Abstract

The Amphiprion (anemonefish or clownfish) family of teleost fish, which is not a common model species, exhibits multiple unique characteristics, including social control of body size and protandrous sex change. The social changes in sex and body size are modulated by neuropeptide signaling pathways. These neuropeptides are formed from complex processing from larger prohormone proteins; understanding the neuropeptide complement requires information on complete prohormones sequences. Genome and transcriptome information within and across 22 teleost fish species, including 11 Amphiprion species, were assembled and integrated to achieve the first comprehensive survey of their prohormone genes. This information enabled the identification of 175 prohormone isoforms from 159 prohormone proteins across all species. This included identification of 9 CART prepropeptide genes and the loss of insulin-like 5B and tachykinin precursor 1B genes in Pomacentridae species. Transcriptome assemblies generally detected most prohormone genes but provided fewer prohormone genes than genome assemblies due to the lack of expression of prohormone genes or specific isoforms and tissue sampled. Comparisons between duplicate genes indicated that subfunctionalization, degradation, and neofunctionalization may be occurring between all copies. Characterization of the prohormone complement lays the foundation for future peptidomic investigation of the molecular basis of social physiology and behavior in the teleost fish.

Changes in Neuropeptide Prohormone Genes among Cetartiodactyla Livestock and Wild Species Associated with Evolution and Domestication

“…The Cetartiodactyla species tree was virtually identical to the expected tree [ 6 , 44 , 45 ]. The strategy of using evolutionary proximal species for gene prediction in weaker assemblies [ 46 ] enabled the recovery of sequences and the results indicated overall sequence consistency across taxonomic groups. The evolutionary proximal strategy minimized the identification of differences between species that could be a result of assembly limitations.…”

Comparative Analysis of Neuropeptides in Homologous Interneurons and Prohormone Annotation in Nudipleuran Sea Slugs

“…For each species, prohormone annotations were performed on publicly available de novo RNA transcriptome assemblies from the NCBI Sequence Read Archive ( Kodama et al, 2012 ; Christie, 2017 ; Southey et al, 2020 ). Species-specific information is as follows: H. crassicornis – SRR1719366 ( Goodheart et al, 2017 ), M. leonina – SRR1950947 and SRR3738852 ( Goodheart et al, 2017 ), and P. californica – SRR026692, SRR026693, SRR026694, SRR026695, SRR1505130, and SRR3928990 ( Zapata et al, 2014 ).…”

Epigenetic Regulation and Environmental Sex Determination in Cichlid Fishes

“…What they lack is a rigorous phylogenetic comparative approach at the mechanistic level with which to explore the evolution of mechanisms mediating sex change and transdetermination. Though more is known at behavioral and physiological levels [Kazancıoğlu and Alonzo, 2010;Erisman et al, 2013], such comparative approaches at the genetic and even epigenetic level have begun in wrasses [Kuwamura et al, 2020], gobies [Sunobe et al, 2017], and clownfish [Southey et al, 2020]. Thus far, findings suggest that key components of the molecular machinery controlling gonadal sex change are phylogenetically conserved at the family level, while neural pathways governing behavioral sex change may be more variable [Thomas et al, 2019].…”