The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish

Authors: BAO, LISUI - Auburn University; TIAN, CHANGXU - Auburn University; LIU, SHIKAI - Auburn University; ZHANG, YU - Auburn University; ELASWAD, AHMED - Auburn University; KHALIL, KARIM - Auburn University; SUN, FANYUE - Auburn University; YUNG, Y - Auburn University; ZHOU, T - Auburn University; LI, N - Auburn University; TAN, S - Auburn University; ZENG, Q - Auburn University; LIU, Y - Auburn University; LI, YUERU - Auburn University; GOA, D - Auburn University; DUNHAM, REX - Auburn University; DAVIS, KENNETH - Retired ARS Employee; Waldbieser, Geoffrey - Geoff; LIU, ZHANJIANG - Syracuse University

Submitted to: BMC Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/9/2019
Publication Date: 1/25/2019
Citation: Bao, L., Tian, C., Liu, S., Zhang, Y., Elaswad, A., Khalil, K., Sun, F., Yung, Y., Zhou, T., Li, N., Tan, S., Zeng, Q., Liu, Y., Li, Y., Goa, D., Dunham, R., Davis, K., Waldbieser, G.C., Liu, Z. 2019. The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biology. 17:6.

Interpretive Summary: Channel catfish utilize an XY sex determination system in which XY fish are male and XX fish are female, but the gene controlling sexual differentiation is unknown. Scientists at Auburn University and the USDA/ARS/Warmwater Aquaculture Research Unit in Stoneville, MS, utilized testosterone to sex-reverse catfish to females, identified XY females using molecular tools, and mated them with normal XY males. YY male offspring were identified using molecular markers and progeny testing. We then produced a genome assembly from a YY male to obtain the Y chromosome sequence. Comparison with the reference genome X chromosome showed no difference in gene content. However, RNA sequence analysis revealed a transcript from the BCAR1 gene was differentially expressed in males during the critical time of differentiation of gonadal tissues. A gene editing experiment provided functional evidence that disruption of the BCAR1 gene in genetic males led to a female phenotype. These results will be used to develop accurate markers to identify genetic sex at an early age and provide a target for identification of the sex determining gene in blue catfish. Culture of only blue catfish males would increase the efficiency of hybrid catfish production.

Technical Abstract: Channel catfish (Ictalurus punctatus) has a XY male heterogametic sex determination system, but the molecular basis of its sex determination is unknown. Thus, generation of a high-quality assembly of the sex chromosome sequences is a crucial step for the understanding of sex determination. Using an innotative approach of a YY channel catfish as a sequencing template and third generation sequencing technologies, we generated, assembled and annotated the YY genome sequence of channel catfish. This represents the very first Y chromosome sequence among teleost fish, and one of the few Y chromosome sequences among vertebrate species. The genome sequence assembly had a contig N50 size of 2.7'Mb and a scaffold N50 size of 26.7'Mb. Genetic linkage and GWAS analyses placed the sex determination locus within a genetic distance less than 0.5 cM and physical distance of 8.9 Mb. However, comparison of the channel catfish X and Y chromosome sequences showed no sex-specific genes. Comparative RNA-Seq analysis between females and males revealed exclusive sex-specific expression of an isoform of BCAR1 in the male during early sex differentiation. Coupling of positional and expression candidates suggest the candidacy of BCAR1 as the sex determination gene, and experimental knockout of BCAR1 demonstrated genetic males (XY) with a female phenotype. Thus the present research supports BCAR1 as a candidate locus for sex determination in channel catfish.