Journal of Tropical Oceanography >
Analysis of differential expressed genes from Charonia tritonis based on transcriptome sequencing
Copy editor: YAO Yantao
Received date: 2022-09-20
Revised date: 2022-10-17
Online published: 2022-10-13
Supported by
National Natural Science Foundation of China(42176129)
Natural Science Foundation of Guangdong Province(2022A1515010779)
The giant triton snail (Charonia tritonis), an endangered gastropod species of ecological and economic importance, is widely distributed in coral reef ecosystems of the Indo-West Pacific region and the tropical waters of the South China Sea. Research on molecular mechanisms is limited due to the lack of complete genomic data for this species. In the present work, transcriptome sequencing of foot muscle and mantle in C. tritonis were obtained by Illumina HiSeq sequencing platform, from which 7994 (3196 upregulated and 4798 downregulated) differentially expressed genes (DEGs) containing biomineralization sequences were identified. The top 20 GO terms in the molecular function category were considered to be related to biomineralization. In KEGG classifications, DEGs are primarily enriched in some pathways that may be involved in biomineralization. The results of qPCR showed that three of the eight genes examined are significantly up-regulated in the mantle. Our results improve the understanding of biomineralization in C. tritonis and provide fundamental transcriptome information to study other molecular mechanisms, such as reproduction.
Key words: Charonia tritonis; transcriptome; DEG
LIU Wenguang , ZHANG Gege , CEN Xitong , HE Maoxian . Analysis of differential expressed genes from Charonia tritonis based on transcriptome sequencing[J]. Journal of Tropical Oceanography, 2023 , 42(4) : 146 -154 . DOI: 10.11978/2022197
表1 转录组数据组装结果统计Tab. 1 Assembly result of transcriptome data |
样本名称 | 总数/个 | 总长度/bp | 平均长度/bp | N50长度/bp | N70长度/bp | GC碱基对数量/% |
---|---|---|---|---|---|---|
法螺肌肉 | 87443 | 50845674 | 581 | 799 | 426 | 43.26 |
法螺外套膜 | 81100 | 48450379 | 597 | 843 | 442 | 43.78 |
All-Unigene | 109722 | 70289861 | 640 | 995 | 485 | 43.43 |
表2 基因注释数量统计Tab. 2 Number of Unigene annotated in NR, NT, Swissprot, KEGG, GO and InterPro database |
总数 | NR | NT | Swissport | KEGG | KOG | InterPro | GO | Intersection | Overall | |
---|---|---|---|---|---|---|---|---|---|---|
基因个数 | 109722 | 26050 | 27059 | 16944 | 18705 | 15319 | 17617 | 9788 | 2712 | 46239 |
注释比例 | 100% | 23.74% | 24.66% | 15.44% | 17.05% | 13.96% | 16.06% | 8.92% | 2.47% | 42.14% |
注: Intersection指的是7个数据库中同时存在的Unigene的数量和比例; Overall为7个数据库中所有数据库注释上的Unigene总数及比例 |
图5 差异表达基因的qPCR验证结果各子图标题中: CA表示carbonic anhydrase(碳酸酐酶), BMP表示bone morphogenetic protein(骨形成蛋白), BAMBI表示BMP and activin membrane bound inhibitor(BMP和激活素膜结合抑制剂), CHIL表示chitinase-like lectin(几丁质酶样凝集素), CHI3L表示chitinase-3-like protein(壳多糖酶3样蛋白); 括号中注明的是相关基因的ID Fig. 5 Relative mRNA expression profiles of biomineralization-related genes of C. tritonis |
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