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De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.
PLoS One. 2014; 9(2):e88589.Plos

Abstract

Assessing the impact of global warming on the food web of the North Atlantic will require difficult-to-obtain physiological data on a key copepod crustacean, Calanus finmarchicus. The de novo transcriptome presented here represents a new resource for acquiring such data. It was produced from multiplexed gene libraries using RNA collected from six developmental stages: embryo, early nauplius (NI-II), late nauplius (NV-VI), early copepodite (CI-II), late copepodite (CV) and adult (CVI) female. Over 400,000,000 paired-end reads (100 base-pairs long) were sequenced on an Illumina instrument, and assembled into 206,041 contigs using Trinity software. Coverage was estimated to be at least 65%. A reference transcriptome comprising 96,090 unique components ("comps") was annotated using Blast2GO. 40% of the comps had significant blast hits. 11% of the comps were successfully annotated with gene ontology (GO) terms. Expression of many comps was found to be near zero in one or more developmental stages suggesting that 35 to 48% of the transcriptome is "silent" at any given life stage. Transcripts involved in lipid biosynthesis pathways, critical for the C. finmarchicus life cycle, were identified and their expression pattern during development was examined. Relative expression of three transcripts suggests wax ester biosynthesis in late copepodites, but triacylglyceride biosynthesis in adult females. Two of these transcripts may be involved in the preparatory phase of diapause. A key environmental challenge for C. finmarchicus is the seasonal exposure to the dinoflagellate Alexandrium fundyense with high concentrations of saxitoxins, neurotoxins that block voltage-gated sodium channels. Multiple contigs encoding putative voltage-gated sodium channels were identified. They appeared to be the result of both alternate splicing and gene duplication. This is the first report of multiple NaV1 genes in a protostome. These data provide new insights into the transcriptome and physiology of this environmentally important zooplankter.

Authors+Show Affiliations

Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.Department of Biological Sciences, Ohio University, Athens, Ohio, United States of America.National Center for Genome Analysis Support, UITS, Indiana University, Bloomington, Indiana, United States of America.Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

24586345

Citation

Lenz, Petra H., et al. "De Novo Assembly of a Transcriptome for Calanus Finmarchicus (Crustacea, Copepoda)--the Dominant Zooplankter of the North Atlantic Ocean." PloS One, vol. 9, no. 2, 2014, pp. e88589.
Lenz PH, Roncalli V, Hassett RP, et al. De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean. PLoS One. 2014;9(2):e88589.
Lenz, P. H., Roncalli, V., Hassett, R. P., Wu, L. S., Cieslak, M. C., Hartline, D. K., & Christie, A. E. (2014). De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean. PloS One, 9(2), e88589. https://doi.org/10.1371/journal.pone.0088589
Lenz PH, et al. De Novo Assembly of a Transcriptome for Calanus Finmarchicus (Crustacea, Copepoda)--the Dominant Zooplankter of the North Atlantic Ocean. PLoS One. 2014;9(2):e88589. PubMed PMID: 24586345.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean. AU - Lenz,Petra H, AU - Roncalli,Vittoria, AU - Hassett,R Patrick, AU - Wu,Le-Shin, AU - Cieslak,Matthew C, AU - Hartline,Daniel K, AU - Christie,Andrew E, Y1 - 2014/02/19/ PY - 2013/12/17/received PY - 2014/01/13/accepted PY - 2014/3/4/entrez PY - 2014/3/4/pubmed PY - 2014/12/30/medline SP - e88589 EP - e88589 JF - PloS one JO - PLoS One VL - 9 IS - 2 N2 - Assessing the impact of global warming on the food web of the North Atlantic will require difficult-to-obtain physiological data on a key copepod crustacean, Calanus finmarchicus. The de novo transcriptome presented here represents a new resource for acquiring such data. It was produced from multiplexed gene libraries using RNA collected from six developmental stages: embryo, early nauplius (NI-II), late nauplius (NV-VI), early copepodite (CI-II), late copepodite (CV) and adult (CVI) female. Over 400,000,000 paired-end reads (100 base-pairs long) were sequenced on an Illumina instrument, and assembled into 206,041 contigs using Trinity software. Coverage was estimated to be at least 65%. A reference transcriptome comprising 96,090 unique components ("comps") was annotated using Blast2GO. 40% of the comps had significant blast hits. 11% of the comps were successfully annotated with gene ontology (GO) terms. Expression of many comps was found to be near zero in one or more developmental stages suggesting that 35 to 48% of the transcriptome is "silent" at any given life stage. Transcripts involved in lipid biosynthesis pathways, critical for the C. finmarchicus life cycle, were identified and their expression pattern during development was examined. Relative expression of three transcripts suggests wax ester biosynthesis in late copepodites, but triacylglyceride biosynthesis in adult females. Two of these transcripts may be involved in the preparatory phase of diapause. A key environmental challenge for C. finmarchicus is the seasonal exposure to the dinoflagellate Alexandrium fundyense with high concentrations of saxitoxins, neurotoxins that block voltage-gated sodium channels. Multiple contigs encoding putative voltage-gated sodium channels were identified. They appeared to be the result of both alternate splicing and gene duplication. This is the first report of multiple NaV1 genes in a protostome. These data provide new insights into the transcriptome and physiology of this environmentally important zooplankter. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/24586345/De_novo_assembly_of_a_transcriptome_for_Calanus_finmarchicus__Crustacea_Copepoda___the_dominant_zooplankter_of_the_North_Atlantic_Ocean_ L2 - https://dx.plos.org/10.1371/journal.pone.0088589 DB - PRIME DP - Unbound Medicine ER -