Journal of Genetics

, Volume 97, Issue 4, pp 995–999 | Cite as

De novo sequencing of the Antarctic krill (Euphausia superba) transcriptome to identify functional genes and molecular markers

  • Chunyan Ma
  • Hongyu Ma
  • Guodong Xu
  • Chunlei Feng
  • Lingbo Ma
  • Lumin Wang
Research Note


To provide massive genetic resources for the Antarctic krill (Euphausia superba), we sequenced and analysed the transcriptome by using high-throughput Illumina paired-end sequencing technology. A total of 77.1 million clean reads representing \(\sim \)11.0 Gb data were generated. The average length of these reads was 142 bp. De novo assembly yielded 125,211 transcripts with a N50 of 690 bp. Further analysis produced 106,250 unigenes, of which 31,683 were annotated based on protein homology searches against protein databases. Gene ontology analysis showed that ion binding, organic substance, metabolic process, and cell part were the most abundantly used terms in molecular function, biological process and cellular component categories, respectively. In addition, 3067 unigenes were mapped onto 311 signal pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, 15,224 simple sequence repeats were identified from 13,535 transcripts, and 103,593 single-nucleotide polymorphisms were found from 21.6% of total transcripts. These genetic resources obtained in this study forms a good foundation for investigating gene function, and evaluating population genetic diversity for this important Southern Ocean fisheries resource, E. superba.


transcriptome resource de novo assembly gene annotation molecular markers Euphausia superba 



This work was supported by the National Science and Technology Support Plan (no. 2013BAD13B03), the National Programme for Support of Top-notch Young Professionals, and the National Natural Science Foundation of China (no. 41406190).


  1. Atkinson A., Siegel V., Pakhomov E. and Rothery P. 2004 Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature  432, 100–103.CrossRefPubMedGoogle Scholar
  2. Auerswald L., Meyer B., Teschke M., Hagen W. and Kawaguchi S. 2015 Physiological response of adult Antarctic krill, Euphausia superba, to long-term starvation. Polar Biol.  38, 763–780.CrossRefGoogle Scholar
  3. Candeias R., Teixeira S., Duarte C. M. and Pearson G. A. 2014 Characterization of polymorphic microsatellite loci in the Antarctic krill Euphausia superba. BMC Res. Notes  7, 73.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Clark M. S., Thorne M. A. S., Toullec J. Y., Meng Y., Guan L. L., Peck L. S. et al. 2011 Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome. PLoS One  6, e15919.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Du H., Bao Z., Hou R., Wang S., Su H., Yan J. et al. 2012 Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867). PLoS One  7, e33311.CrossRefPubMedPubMedCentralGoogle Scholar
  6. Feng N., Ma H., Ma C., Xu Z., Li S., Jiang W. et al. 2014 Characterization of 40 single nucleotide polymorphism (SNP) via \(T_{{\rm m}}\)-shift assay in the mud crab (Scylla paramamosain). Mol. Biol. Rep.  41, 5467–5471.CrossRefPubMedGoogle Scholar
  7. Fielding S., Watkins J. L., Trathan P. N., Enderlein P., Waluda C. M., Stowasser G. et al. 2014 Inter annual variability in Antarctic krill (Euphausia superba) density at South Georgia, Southern Ocean: 1997–2013. ICES J. Mar. Sci.  71, 2578–2588.CrossRefGoogle Scholar
  8. Hou R., Bao Z., Wang S., Su H., Li Y., Du H. et al. 2011 Transcriptome sequencing and de novo analysis for yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS One  6, e21560.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Hunt B. J., Özkaya Ö., Davies N. J., Davies N. J., Gaten E., Seear P. et al. 2017 The Euphausia superba transcriptome database, SuperbaSE: an online, open resource for researchers. Ecol. Evol.  7, 6060–6077.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Jeffery N. W. 2012 The first genome size estimates for six species of krill (Malacostraca, Euphausiidae): large genomes at the north and south poles. Polar Biol.  35, 959–962.CrossRefGoogle Scholar
  11. Jia Z., Virtue P., Swadling K. M. and Kawaguchi S. 2014 A photographic documentation of the development of Antarctic krill (Euphausia superba) from egg to early juvenile. Polar Biol.  37, 165–179.CrossRefGoogle Scholar
  12. Koh H. Y., Lee J. H., Han S. J., Park H., Shin S. C. and Lee S. G. 2015 A transcriptomic analysis of the response of the arctic pteropod Limacina helicina to carbon dioxide-driven seawater acidification. Polar Biol.  38, 1727–1740.CrossRefGoogle Scholar
  13. Liao X., Cheng L., Xu P., Lu G., Wachholtz M., Sun X. et al. 2013 Transcriptome analysis of crucian carp (Carassius auratus), an important aquaculture and hypoxia-tolerant species. PLoS One  8, e62308.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Ma H. Y., Ma C. Y., Li S. J., Jiang W., Li X. C., Liu Y. X. et al. 2014 Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery. PLoS One  9, e102668.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Martins M. J. F., Lago-Leston A., Anjos A., Duarte C. M., Agusti S., Serrao E. A. et al. 2015 A transcriptome resource for Antarctic krill (Euphausia superba Dana) exposed to short-term stress. Mar. Genomics  23, 45–47.CrossRefPubMedGoogle Scholar
  16. Meyer B. 2012 The overwintering of Antarctic krill, Euphausia superb, from an ecophysiological perspective. Polar Biol.  35, 15–37.CrossRefGoogle Scholar
  17. Meyer B., Martini P., Biscontin A., de Pitta C., Romualdi C., Teschke M. et al. 2015 Pyrosequencing and de novo assembly of Antarctic krill (Euphausia superba) transcriptome to study the adaptability of krill to climate-induced environmental changes. Mol. Ecol. Resour.  15, 1460–1471.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Muriira N. G., Xu W., Muchugi A., Xu J. and Liu A. 2015 De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). BMC Genomics  16, 723.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Sales G., Deagle B. E., Calura E., Martini P., Biscontin A., De Pittà C. et al. 2017 KrillDB: a de novo transcriptome database for the Antarctic krill (Euphausia superba). PLoS One  12, e0171908.CrossRefPubMedPubMedCentralGoogle Scholar
  20. Shi Y., Sun S., Li C. and Tao Z. 2014 Population distribution, structure and growth condition of Antarctic krill (Euphausia superb Dana) during the austral summer in the Southern Ocean. Adv. Polar Sci.  25, 183–191.Google Scholar
  21. Sun H., Liu Y., Gai Y., Geng J., Chen L., Liu H. et al. 2015 De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation. BMC Genomics  16, 652.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Indian Academy of Sciences 2018

Authors and Affiliations

  1. 1.East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiPeople’s Republic of China
  2. 2.Guangdong Provincial Key Laboratory of Marine BiologyShantou UniversityShantouPeople’s Republic of China

Personalised recommendations