Identification, Expression and Evolution of Short-Chain Dehydrogenases/Reductases in Nile Tilapia (Oreochromis niloticus).

Shuai Zhang,Deshou Wang,Baoyue Lu,Shuqing Zheng,Wenjing Tao,Thomas D Kocher,Lang Xie,Linyan Zhou,Xiaoshuang Wang

doi:10.3390/ijms22084201

Abstract

The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

Highlights

Short-chain dehydrogenases/reductases (SDR) superfamily comprises NAD(P)(H)dependent oxidoreductases that possess the conserved Rossmann-fold motif
119 short-chain dehydrogenases/reductases (SDR) were identified in the Nile tilapia genome
In order to distinguish genes derived from different rounds of whole genome duplication (WGD) or tandem duplication, we developed a new system of nomenclature by adding numbers or letters as suffixes of the gene name

Summary

Introduction

Short-chain dehydrogenases/reductases (SDR) superfamily comprises NAD(P)(H)dependent oxidoreductases that possess the conserved Rossmann-fold motif They are a large and ancient gene family found in organisms as diverse as viruses and vertebrates [1].With the rapid release of genome databases for numerous species, the size of the SDR superfamily has grown considerably since the initial family members were characterized in the late 19700 s [2,3,4,5]. The diversification and the morphological innovations of vertebrates are attributed to large-scale gene or genome duplications at the origin of the group. Fish represent the largest and the most diverse group of vertebrates, comprehensive identification and genome-wide study on the SDR superfamily are still lacking.

Methods

Discussion

Conclusion