Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sample Collection and RNA Isolation
2.3. cDNA Synthesis and HiSeq 2500 Sequencing
2.4. De Novo Assembly and Assessment of De Novo Assemblies
2.5. Transcriptome Annotation
2.6. Identification of SSRs
3. Results
3.1. Illumina Reads and Sequence Assembly
3.2. Sequence Annotation of Unigenes
3.3. KOG, GO and KEGG Classifications
3.4. Development and SSR Locus Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Acknowledgements
Author Contributions
Conflicts of Interest
References
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Total Number of Raw Reads | |
Number of sequences | 323,319,608 |
Number of bases | 40,738,270,608 |
Total number of clean reads | |
Number of sequences | 318,610,596 |
Number of bases | 39,745,513,470 |
Mean length of contig (bp) | 124.7 |
N50 length of contig (bp) | 126 |
GC % of contig | 48.39 |
High-quality reads (%) | 98.54 (sequences), 97.56 (bases) |
Contig information | |
Total number of contig | 269,822 |
Number of bases | 192,327,026 |
Mean length of contig (bp) | 712.8 |
N50 length of contig (bp) | 1148 |
GC % of contig | 46.82 |
Largest contig (bp) | 40,450 |
No. of large contigs (≥500 bp) | 89,407 |
Unigene information | |
Total number of unigenes | 208,813 |
Number of bases | 146,173,633 |
Mean length of unigene (bp) | 700.0 |
N50 length of unigene (bp) | 1089 |
GC % of unigene | 46.97 |
Length ranges (bp) | 224–40,450 |
Databases | All | ≤300 bp | 300–1000 bp | ≥1000 bp |
---|---|---|---|---|
PANM-DB | 87,719 | 20,029 | 43,958 | 23,732 |
UNIGENE | 26,845 | 6231 | 12,885 | 7729 |
KOG | 63,978 | 12,955 | 30,892 | 20,131 |
GO | 57,731 | 12,915 | 28,153 | 16,663 |
KEGG | 7247 | 1735 | 3400 | 2112 |
ALL | 95,105 | 22,935 | 48,081 | 24,089 |
SSR parameters | Number |
---|---|
Total number of sequences examined | 29,547 |
Total size of examined sequences (bp) | 75,658,821 |
Total number of identified SSRs | 1595 |
Di-nucleotide | 529 |
Tri-nucleotide | 862 |
Tetra-nucleotide | 144 |
Penta-nucleotide | 33 |
Hexa-nucleotide | 27 |
Number of SSR containing sequences | 1432 |
Number of sequences containing more than 1 SSR | 140 |
Number of SSRs present in compound formation | 74 |
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Seong, J.; Kang, S.W.; Patnaik, B.B.; Park, S.Y.; Hwang, H.J.; Chung, J.M.; Song, D.K.; Noh, M.Y.; Park, S.-H.; Jeon, G.J.; et al. Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery. Genes 2016, 7, 114. https://doi.org/10.3390/genes7120114
Seong J, Kang SW, Patnaik BB, Park SY, Hwang HJ, Chung JM, Song DK, Noh MY, Park S-H, Jeon GJ, et al. Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery. Genes. 2016; 7(12):114. https://doi.org/10.3390/genes7120114
Chicago/Turabian StyleSeong, Jiyeon, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, and et al. 2016. "Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery" Genes 7, no. 12: 114. https://doi.org/10.3390/genes7120114
APA StyleSeong, J., Kang, S. W., Patnaik, B. B., Park, S. Y., Hwang, H. J., Chung, J. M., Song, D. K., Noh, M. Y., Park, S.-H., Jeon, G. J., Kong, H. S., Kim, S., Hwang, U. W., Park, H. S., Han, Y. S., & Lee, Y. S. (2016). Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery. Genes, 7(12), 114. https://doi.org/10.3390/genes7120114