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. 2014 Oct 10;9(10):e109419.
doi: 10.1371/journal.pone.0109419. eCollection 2014.

Transcriptome analysis of the Trachinotus ovatus: identification of reproduction, growth and immune-related genes and microsatellite markers

Xie Zhenzhen  1 , Xiao Ling  1 , Wang Dengdong  1 , Fang Chao  1 , Liu Qiongyu  1 , Li Zihao  1 , Liu Xiaochun  1 , Zhang Yong  1 , Li Shuisheng  1 , Lin Haoran  2
Affiliations

Transcriptome analysis of the Trachinotus ovatus: identification of reproduction, growth and immune-related genes and microsatellite markers

Xie Zhenzhen et al. PLoS One. .

Abstract

Background: The Trachinotus ovatus (Teleostei, Carangidae) is an economically important marine fish species in the world. However, the lack of genomic information regarding this species limits our understanding of the genetics and biological mechanisms in Trachinotus ovatus. In this study, high throughput transcriptome sequencing was used to obtain comprehensive genomic information in Trachinotus ovatus.

Principal findings: Transcriptome sequencing was performed by using Illumina paired-end sequencing technology. The 98,534,862 high quality reads were yielded, and were de novo assembled into 156,094 unigenes with an average sequence length of 1179 bp. Transcriptome annotation revealed that 75,586 and 67,923 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 67,923 unigenes were grouped into 25 Cluster of Orthologous Groups (COG) functional categories, 37,976 unigenes were clustered into 61 Gene Ontology (GO) terms, and 38,172 unigenes were assigned to 275 different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Based on the transcriptome dataset, a large number of unigenes associated with reproduction, growth and immunity were identified. Furthermore, a total number of 38,794 simple sequence repeats (SSRs) were discovered and 16 polymorphic loci were characterized in Trachinotus ovatus.

Conclusion/significance: The present study is the first transcriptome analysis of a fish species belonging to the genus Trachinotus and provides a valuable genomic resource for novel gene discovery, gene expression and regulation studies, and the identification of genetic markers in Trachinotus ovatus and the other fish of the genus Trachinotus.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Length distribution of all unigenes of Trachinotus ovatus.
Figure 2
Figure 2. Comparison of Trachinotus ovatus unigenes to Danio rerio orthologous coding sequences.
(A) The ratio of Trachinotus ovatus unigene length to Danio rerio ortholog length was plotted against Trachinotus ovatus unigene coverage depth. (B) The total percentage of Danio rerio ortholog coding sequence covered by all Trachinotus ovatus unigenes.
Figure 3
Figure 3. Venn diagram of annotation results against Nr, SwissProt, COG and KEGG databases.
The number in each color block indicates the number of unigenes that is annotated by single or multiple databases.
Figure 4
Figure 4. Top-hit species distribution for sequences from Trachinotus ovatus submitted BLASTX against the NCBI-Nr database.
Only fish species were present in this study.
Figure 5
Figure 5. Clusters of Orthologous Groups (COG) functional classification of the Trachinotus ovatus transcriptome.
Figure 6
Figure 6. Gene Ontology (GO) analysis and functional classification of the Trachinotus ovatus transcriptome.
Figure 7
Figure 7. Frequency of classified repeat types of SSRs.
See this image and copyright information in PMC

References

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