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Database News

16-09-2016: New holotype sequences: Hamacantha cassanoi Lehnert & Stone 2016 (#1646) added.

15-09-2016: New Reference (Paratype) Clathria (Wilsonella) rugosa Hooper & Levi 1993 (#652)

2016: New Sponge barcoding app in final phase. Watch this space! See preview

19-05-2016: Holotype of Isabella mirabilis (#1642) and Holo- & Paratypes of I. tanoa Ekins et al. 2016 (#1643-1645) added.

22-12-2015: Demosponge CO1 and 28S data of Erpenbeck et al.  Molecular biodiversity of Red Sea demosponges. Marine Pollution Bulletin (2016) added.

20-12-2015: Calcarea data of Voigt et al. (2016) A short LSU rRNA fragment as a standard marker for integrative taxonomy in calcareous sponges (Porifera: Calcarea) added.

10-08-2015: Antarctic sponge data of Vargas et al. (2015) Diversity in a Cold Hot-Spot: DNA - Barcoding Reveals Patterns of Evolution among Antarctic Demosponges (Class Demospongiae, Phylum Porifera), PLoS ONE added.

22-07-2015: New Holotype data added as References: Heteroxya corticata (#1152), Narrabeena lamellata (#1160), Stelletta anthastra (#1161). from Erpenbeck et al. (2015) Nothing in (sponge) biology makes sense – except when based on holotypes.

01-05-2015: Data of Schuster et al. (2015) Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges added

20-02-2015: New References: Isabella harborbranchi (#1114-1117) from Carvalho et al. (2014) Lithistid sponges of the upper bathyal of Madeira, Selvagens and Canary Islands, with description of a new species of Isabella

03-07-2012: Workflow and results of the Sponge Barcoding Project in PLoS ONE: Vargas et al.: Barcoding Sponges: An Overview Based on Comprehensive Sampling. (open access)

01-04-2012: New astrophorid sequences of Cárdenas & Rapp (2012): A review of Norwegian streptaster-bearing Astrophorida (Porifera: Demospongiae: Tetractinellida), new records and a new species; Zootaxa 3253: 1–52 added.

08-01-2012: New halichondrid sequences added from Erpenbeck et al. (2012) The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data. The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data. Organisms Diversity & Evolution 12:57-70.

16-11-2011: Implementation of the Geneious Biocode LIMS for handling sponge barcoding data. (pdf)

04-11-2011: Several taxonomy updates on submitted specimens.

October 2011: Several edits of metadata performed.

27-06-2011: New reference record of Sigmaxinella (S. hipposiderus) and two other specimens from Mitchell et al. 2011 Zootaxa added.

26-06-2011: The Sponge Barcoding Project is featured by Geneious (read more).

February 2011: two new reference records of Halisarca species from Ereskovsky et al. 2001 Zootaxa added.

October 2010: Search interface (BLAST etc.) in development

Data of Xavier et al. (2010) and Ferrario et al. (2010) added.

More than 500 records/sequences uploaded.

06-06-2010: New reference specimen for Tethya leysae added.

June 2010: High throughput DNA extraction, PCR and sequencing of Queensland Museum tissue samples in progress.

14-05-2010: Major additions to the database expected in the near future due to significant funding from the Marine Barcode of Life Project.

 

Primers Print E-mail

The standard barcoding fragment for the Barcoding of Life initiative is a ~ 640 bp long fragment located at the 5' site of the mitochondrial cytochrome oxidase subunit 1 (CO1). However, as this fragment might not display sufficient variability in sponges [1][2], we suggest sequencing an additional downstream region, which exhibits a higher substitution rate [3] in order to obtain a fragment of about 1,100 bp with a higher number of variable sites. A submission ITS-1 and 2 sequences, which could be added to the CO1-sequence tag, is also encouraged.

 

 

 

Standard barcoding primer from Folmer et al. [4]:

LCO1490: GGT CAA CAA ATC ATA AAG ATA TTG G

HCO2198:TAA ACT TCA GGG TGA CCA AAA AAT CA

 

Degenerated Folmer et al. [4] (standard) barcoding primer designed by Meyer et al. [5]:

dgLCO1490: GGT CAA CAA ATC ATA AAG AYA TYG G

dgHCO2198:TAA ACT TCA GGG TGA CCA AAR AAY CA

 

Primers from Rot et al. [6]:

COX1-R1: TGT TGR GGG AAA AAR GTT AAA TT

COX1-D2: AAT ACT GCT TTT TTT GAT CCT GCC GG

 

Primers for the extended fragment, designed by Misof et al. [7] and Erpenbeck et al. [8]:
(Suggested in a nested approach in which the C1J2165/C1Npor2760 PCR-product will be reamplified by CO1porF1/CO1porR1. See [8] for details.)

CO1porF1:CCN CAN TTN KCN GMN AAA AAA CA

CO1porR1: AAN TGN TGN GGR AAR AAN G

C1Npor2760: TCT AGG TAA TCC AGC TAA ACC

C1J2165: GAA GTT TAT ATT TTA ATT TTA CCN GG

 

References (also available upon request at This e-mail address is being protected from spambots. You need JavaScript enabled to view it ):

[1] Duran, S. & Rützler, K. (2006) Molecular Phylogenetics and Evolution 40(1), 292-297.

[2] Wörheide, G. (2006) Marine Biology 148, 907-912.

[3] Erpenbeck, D., Hooper, J. N. A. & Wörheide, G. (2006) Molecular Ecology Notes 6, 550–553.

[4] Folmer O, Black M, Hoeh W, Lutz R & Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome C oxidase subunit I from diverse metazoan invertebrates. :. Mol. Mar. Biol. Biotechnol. 3: 294-299.

[5] Meyer CP, Geller JB & Paulay G (2005) Fine scale endemism on coral reefs: Archipelagic differentiation in turbinid gastropods. Evolution 59: 113-125.

[6] Rot C, Goldfarb I, Ilan M & Huchon D (2006) Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria. Bmc Evolutionary Biology 6

[7] Misof B, Erpenbeck D & Sauer KP (2000) Mitochondrial gene fragments suggest paraphyly of the genus Panorpa (Mecoptera, Panorpidae). Molecular Phylogenetics and Evolution 17: 76-84.

[8] Erpenbeck D, Knowlton AL, Talbot SL, Highsmith RC & Van Soest RWM (2003 (2004)) A molecular comparison of Alaskan and North East Atlantic Halichondria panicea (Pallas 1766) (Porifera: Demospongiae) populations. Boll. Mus. Ist. Univ. Genova. 68: 319-325.

 

 

 
 
 

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