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Received Jul 25; Accepted Apr This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. This article has been cited by other articles in PMC. Table S2: Genes differentially expressed in C.
Table S3: Go terms of genes differentially expressed in C. Abstract Background Despite their species abundance and primary economic importance, genomic information about copepods is still limited.
Results Copepodid larvae and adults were used as the basic material for transcriptome sequencing. Conclusion Our data provide the most comprehensive transcriptome resource available for C. Introduction Copepods are more abundant than any other multicellular animal group, including the hyper-abundant insects and nematodes [1] , [2].
Results and Discussion Sequencing analysis and assembly Two types of cDNA samples, which represented different developmental stages and adult tissues of C.
Table 1 Summary of the sequencing and assembly of the C. Raw reads bade pairs 1,, ,, Clean reads 1,, Isogroup 19, Isotigs 31, Isotig N50 Mean isotigs per isogroup 1. Open in a separate window. Figure 1. Overview of C. Transcriptome annotation Several complementary approaches were used to annotate the assembled sequences. Figure 2.
Estimating the number of genes expressed in C. Genes involved with development The growth and development of many copepods such as C. Table 3 Selected development process genes identified in the C. Differentially expressed genes Of the whole transcriptome sequences, , reads were generated from the C. Table 4 Expression levels of genes that may be invovled with the diapause regulation of C. ELOV: elongation of very long chain fatty acids protein. FAMeT: farnesoic acid O-methyltransferase.
Gene expression level is calculated by using reads per kilobase of the transcript per million mapped reads RPKM. Figure 3. Real-time PCR validation of differentially expressed genes that may be involved in diapause. Table 5 Oligonucleotide primer sequences for real time PCR. Figure 4. Classification of single nucleotide polymorphisms SNPs indentified in the C. The overall frequency of these SNPs is one per bp.
Conclusions In this work, we performed de novo transcriptome sequencing of C. Materials and Methods Sample preparation and sequencing Copepods were collected from Jiaozhou Bay, China, and brought to the laboratory in fresh seawater.
Sequence data analysis and assembly Prior to assembly, adapter sequences and low-quality sequences were trimmed from the raw reads. Differential gene expression analysis The expression level of a transcript was quantified in reads per kilobase of the transcript per million mapped reads RPKM in the transcriptome [58].
Real-time PCR The significant up- or down- regulated expressed genes associated with diapause were validated and quantified by real-time PCR. XLSX Click here for additional data file. Table S2 Genes differentially expressed in C. Table S3 Go terms of genes differentially expressed in C. DOC Click here for additional data file. References 1. Humes AG How many copepods? Hydrobiologia : 1—7.
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