Zhang Xiujuan, Zhou Jiabin, Li Linmiao, Huang Wenzhong, Ahmad Hafiz Ishfaq, Li Huiming, Jiang Haiying, Chen Jinping
Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China.
Front Zool. 2020 Apr 9;17:11. doi: 10.1186/s12983-020-00355-z. eCollection 2020.
Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, .
A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3028), and completely different KEGG pathways were significantly enriched between the ovary-biased and testis-biased DEUs. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50% (30/60) genes of those showed significantly differential expression in testes and ovaries. Among these, the Amh and Gsdf with testis-biased expression, and the Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of , respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity in early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4339 predicted transcript factors (TFs) were also respectively identified, which were all significantly associated with the early gametogenesis of .
Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of in the early gametogenesis stage, which could provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.
鲟鱼（鲟形目）是多倍体软骨硬鳞鱼类，是研究脊椎动物发育和进化的重要模式物种。为了更好地理解鲟鱼繁殖调控机制，本研究将PacBio全长转录组测序（Iso-Seq）与Illumina短读长RNA测序方法相结合，以发现参与施氏鲟早期配子发生的全长基因。
从两个SMRT细胞中总共产生了50.04 G的子读数碱基，在此，从7条3岁个体的性腺组织（3个睾丸和4个卵巢）中产生了164,618个非冗余全长转录本（单基因），平均长度为2782 bp。卵巢特异性表达的单基因数量多于睾丸（19,716对3028），并且在卵巢偏向和睾丸偏向的差异表达单基因之间，完全不同的KEGG途径显著富集。重要的是，成功鉴定出60个早期配子发生相关基因（涉及755个单基因），其中恰好50%（30/60）的基因在睾丸和卵巢中表现出显著差异表达。其中，偏向睾丸表达的Amh和Gsdf，以及偏向卵巢表达的Foxl2和Cyp19a分别强烈暗示了它们在施氏鲟精子发生和卵子发生中的重要调控作用。我们还发现了四个新的Sox9转录本变体，这增加了调控基因的数量，并暗示了早期配子发生中的功能复杂性。最后，总共检测到236,672个可变剪接事件（涉及36,522个单基因）以及10,556个假定的长链非编码RNA（lncRNA）和预测的4339个转录因子（TF），它们均与施氏鲟的早期配子发生显著相关。
总体而言，我们的结果提供了新的全长转录数据的遗传资源和信息，作为鲟鱼基因组水平的参考。至关重要的是，我们探索了施氏鲟在早期配子发生阶段睾丸和卵巢之间不同的综合遗传特征，这可为进一步研究鲟鱼繁殖调控机制提供候选基因和理论基础。
