BMC genomics — 2017 — Oreochromis niloticus (Nile Tilapia) — sex determination regions

Sex deter­mi­na­tion regions

The new O_niloti­cus_UMD1 assem­bly was used to study sequence dif­fer­en­ti­a­tion across two sex-deter­min­ing regions in tilapi­as. The first region is an XX/XY sex-deter­mi­na­tion region on LG1 found in many strains of til-apia [9, 34, 44–47]. We pre­vi­ous­ly char­ac­ter­ized this region by whole genome Illu­mi­na re-sequenc­ing of pooled DNA from males and females [48]. We realigned the­se sequences to the new O_niloti­cus_UMD1 assem­bly and searched for vari­ants that were fixed in the XX female pool and poly-mor­phic in the XY male pool. Fig­ure 4 shows the FST and the sex-pat­terned vari­ant alle le fre­quen­cies for the XX/XY O. niloti­cus com­par­ison across the com­plete Orenil1.1 and O_niloti­cus_UMD1 assem­blies, while Fig. 5 focus­es on the high­ly dif­fer­en­ti­at­ed ~9Mbp region on LG1 with a sub­stan­tial num­ber of sex-pat­terned vari­ants, indica­tive of a reduc­tion in recom­bi­na­tion in a sex deter­mi­na­tion region that hasexistedforsometime[48].

The sec­ond sex com­par­ison is for an ZZ/WZ sex-deter­mi­na­tion region on LG3 in a strain of O. aureus [11,49]. This region has not pre­vi­ous­ly been char­ac­ter­ized using whole genome sequenc­ing. For this com­par­ison we iden­ti­fied vari­ant alle­les fixed in the ZZ male pool and poly­mor­phic in the WZ female pool. Fig­ure 6 shows the FST and the sex-pat­terned vari­ant allele fre­quen­cies for this com­par­ison across the whole O_niloti­cus_UMD1 assem­bly, while Fig. 7 focus­es on the dif­fer­en­ti­at­ed region on LG3. O. aureus LG3 con­tains a large ~50Mbp region of dif­fer­en­ti­at­ed sex-pat­terned vari­ants, also indica­tive of a reduc­tion in recom­bi­na­tion in the sex deter­mi­na­tion region. Fig­ure 6 also shows this dif­fer­en­ti­a­tion pat­tern on sev­er­al oth­er LGs (LG7, LG9, LG14, LG16, LG18, LG22 and LG23). It is pos­si­ble that the­se small­er regions of sex-pat­terned dif­fer­en­ti­a­tion are actu­al­ly translo­ca­tions in O.aureus rel­a­tive to the O. niloti­cus genome assem­bly.

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