ZooGene - A DNA Sequence Database for Calanoid Copepods and Euphausiids
Entry ID:
zoogene
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Summary
Abstract:
An international partnership created a zooplankton genomic (ZooGene) database of DNA type sequences for calanoid copepods and euphausiids. The ZooGene database was designed to include all species of these groups and to allow expansion to additional zooplankton groups. The ZooGene partnership includes four P.I.s and thirteen expert taxonomic consultants from seven countries. Zooplankton samples are ... sorted from existing archival collections, obtained in coordination with planned oceanographic research efforts, and collected during National Marine Fisheries Service field surveys. The taxonomic experts confirm species' identifications; DNA sequencing is done at the University of New Hampshire and, in some cases, in other partners' laboratories. For each species, a DNA type sequence is determined for a portion of the mitochondrial cytochrome oxidase I (mtCOI) gene; multiple mtCOI sequences are included as necessary to reflect intraspecific variation. The ZooGene database is designed, created, managed, maintained, and distributed as part of the proposed work; the data is integrated into the Ocean Biogeographical Information System (OBIS).
The uses for and research applications of the ZooGene database include uniform standards of species' identification; evaluation of the taxonomic significance of geographic variation within widespread species; identification of cryptic species; accurate estimation of species' diversity; determination of evolutionary relationships among species; and design of rapid molecularly-based species' identification protocols.
Information was obtained from http://www.zoogene.org/. MtDNA sequence variation, and mtCOI in particular, has been shown to be useful to resolve evolutionary relationships among closely-related species groups for a wide range of taxa (Jacobs and Grimes, 1986; Brown et al., 1994; Lunt et al., 1996; Harasewych et al., 1997; see review in Avise, 1994). MtCOI sequences have also been used for population genetic studies for a wide variety of organisms. For most species, variation of mtCOI within a species is far less than variation between species, making the gene a diagnostic molecular systematic character. The selection of mtCOI as a target gene for the ZooGene effort results from previous molecular systematic and population genetic studies of copepods and euphausiids by Ann Bucklin. These studies have revealed mtCOI sequence variation within species to range from 1 - 2%, while variation between species ranged from 10 - 20%g (Bucklin et al., 1998a, 1999, 2000b, unpublished data). Preliminary studies have demonstrated the usefulness of mtCOI sequence data for molecular systematic and population genetic studies of calanoid copepods and euphausiids (Bucklin et al., 1997a, 1997b, 1998a, 1999, 2000a, 2000b). Among the calanoid copepods, we have focused initially on two families: the Calanidae (including 29 species of eight genera; Bradford, 1988) and the Clausocalanidae (including at least 28 species in six genera; Frost and Fleminger, 1968), which together include at least eight sibling species groups. We have recently determined the DNA sequence of a ~ 650 base-pair (bp) region of mtCOI for 19 species of six calanoid genera (Bucklin et al., 1999, unpublished data) using modifications of techniques given in Folmer et al. (1994; and see Bucklin et al., 1999). Sequence differences between calanoid copepod species for this gene portion ranged from 8 - 21% (Bucklin, unpublished data). The mtCOI sequences resolved evolutionary relationships among congeneric species (shown in Fig. 1 [large version] as blue lines). MtCOI sequence variation also discriminated geographic populations of C. helgolandicus (from the Adriatic, North Sea, and Gulf Stream Extension) and C. pacificus (from the California Current and the North Pacific Central Gyre). The selected MtCOI region was too variable to resolve relationships among genera (Bucklin et al., 1999), so a phylogenetic "backbone" - based on the more conserved sequence for nuclear small-subunit16S rRNA - was used to show the relationships among the genera (shown in Fig. 1 as red lines). The ~350 bp region of nuclear 16S rRNA differed by less than 1% between species.
[Note: The phylogenetic tree shown in Fig. 1 was reconstructed by separate analyses of mtCOI and nuclear16S rRNA sequences using the Neighbor Joining algorithm (Kumar et al., 1993). Numbers at branchpoints are bootstrap values.] 
Related URL
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Description:
OBIS Advanced Search Data Extent Map and related function
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Geographic Coverage
(Click for Interactive Map)
Spatial coordinates
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N: 78.0
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S: 54.5
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E: 160.0
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W: 178.51
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Data Set Citation
Dataset Originator/Creator:
Anne Bucklin
Dataset Title:
ZooGene - A DNA Sequence Database for Calanoid Copepods and Euphausiids
Dataset Release Date:
2002
Dataset Release Place:
New Hampshire
Dataset Publisher:
University of New Hampshire
Data Presentation Form:
database
Online Resource:
http://www.zoogene.org/jg/dir/
Temporal Coverage
Start Date:
1989-11-15
Stop Date:
2001-09-02
Quality
ZooGene contains taxonomic information for two groups - calanoid copepods and euphausiids. It is anticipated that other groups of zooplankton will be added to expand the taxonomic coverage.
Access Constraints
None
Use Constraints
Acknowledge the use of specific records from contributing databases in the form appearing in the 'Citation' field thereof (if any); and acknowledge the use of the OBIS facility.
For information purposes, email to obissupport@marine.rutgers.edu the full citation of any publication made (printed or electronic) that cites OBIS or any constituent part.
Recognize the limitations of data in OBIS.
Data Set Progress
IN WORK
Personnel
Role:
TECHNICAL CONTACT
Phone:
603 862-0122
Fax:
603 862-0243
Email:
acb at cisunix.unh.edu
Contact Address:
University of New Hampshire
OPAL/EOS, 142 Morse Hall
City:
Durham
Province or State:
New Hampshire
Postal Code:
03824
Country:
USA
Publications/References
Ann Bucklin, University of New Hampshire Durham, NH; Bruce W. Frost, University of Washington, Seattle, WA; Peter H. Wiebe, Woods Hole Oceanographic Institution, Woods Hole, MA; Michael J. Fogarty, NOAA/NMFS Northeast Fisheries Science Center, Woods Hole, MA ZooGene, a DNA sequence database for calanoid copepods and euphausiids:an OBIS tool for uniform standards of species identification, 2002, SEQ CHAPTER 2001 NOPP Annual Report.
Creation and Review Dates
DIF Creation Date:
2002-10-28
Last DIF Revision Date:
2009-01-09
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