Yuan Jing, Tao Wenjing, Cheng Yunying, Huang Baofeng, Wang Deshou
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, 400715, People's Republic of China.
Fish Physiol Biochem. 2014 Aug;40(4):1239-52. doi: 10.1007/s10695-014-9919-6. Epub 2014 Feb 14.
The fox genes play important roles in various biological processes, including sexual development. In the present study, we isolated 65 fox genes, belonging to 18 subfamilies named A-R, from Nile tilapia through genome-wide screening. Twenty-four of them have two or three (foxm1) copies. Furthermore, 16, 25, 68, and 45 fox members were isolated from nematodes, protochordates, teleosts, and tetrapods, respectively. Phylogenetic analyses indicated fox gene family had undergone three expansions parallel to the three rounds of genome duplication during evolution. We also analyzed the clustered fox genes and found that apparent linkage duplication existed in teleosts, which further supported fish-specific genome duplication hypothesis. In addition, species- and lineage-specific duplication is another reason for fox gene family expansion. Based on the four pairs of XX and XY gonadal transcriptome data from four critical developmental stages, we analyzed the expression profile of all fox genes and identified sexually dimorphic fox genes at each stage. All fox genes were detected in gonads, with 15 of them at the background expression level (total read per kb per million reads, RPKM < 10), 29 at moderate expression level (10 < total RPKM < 100), and 21 at high expression level (total RPKM > 100). There are 27, 24, 28, and 9 sexually dimorphic fox genes at 5, 30, 90, and 180 days after hatching (dah), respectively. foxq1a, foxf1, foxr1, and foxr1 were identified as the most differentially expressed genes at each stage. foxl2 was characterized as XX-dominant gene, while foxd5, foxi3, foxn3, foxj1a, foxj3b, and foxo6b were characterized as XY-dominant genes. qPCR and in situ hybridization of foxh1 and foxj1a were performed to confirm the expression profiles and to validate the transcriptome data. Our results suggest that fox genes might play important roles in sex determination and gonadal development in teleosts.
狐狸基因在包括性发育在内的各种生物学过程中发挥着重要作用。在本研究中，我们通过全基因组筛选从尼罗罗非鱼中分离出65个狐狸基因，它们属于18个命名为A - R的亚家族。其中24个有两个或三个（foxm1）拷贝。此外，分别从线虫、原索动物、硬骨鱼和四足动物中分离出16、25、68和45个狐狸基因成员。系统发育分析表明，狐狸基因家族在进化过程中经历了三次与三轮基因组复制平行的扩张。我们还分析了成簇的狐狸基因，发现硬骨鱼中存在明显的连锁重复，这进一步支持了鱼类特有的基因组复制假说。此外，物种和谱系特异性复制是狐狸基因家族扩张的另一个原因。基于四个关键发育阶段的四对XX和XY性腺转录组数据，我们分析了所有狐狸基因的表达谱，并确定了每个阶段的性别二态性狐狸基因。在性腺中检测到所有狐狸基因，其中15个处于背景表达水平（每千碱基每百万 reads 中的总 reads，RPKM < 10），29个处于中等表达水平（10 < 总 RPKM < 100），21个处于高表达水平（总 RPKM > 100）。在孵化后5、30、90和180天（dah）分别有27、24、28和9个性别二态性狐狸基因。foxq1a、foxf1、foxr1和foxr1被确定为每个阶段差异表达最显著的基因。foxl2被表征为XX显性基因，而foxd5、foxi3、foxn3、foxj1a、foxj3b和foxo6b被表征为XY显性基因。对foxh1和foxj1a进行了qPCR和原位杂交，以确认表达谱并验证转录组数据。我们的结果表明，狐狸基因可能在硬骨鱼的性别决定和性腺发育中发挥重要作用。
