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Marine Turtle mtDNA Longer Sequences (~800 bp)

Loggerhead (Caretta caretta) mitochondrial DNA control region sequences:
Atlantic and Mediterranean

New mtDNA D-Loop primers have been developed for marine turtles (Abreu-Grobois et al. 2006) that yield sequences of ~800bp. The sequences are presented below. The protocol for naming these longer sequences follows:

1. All longer (~800bp) sequence names will be based on the original 380 bp foundation sequence as currently presented on the ACCSTR website [http://accstr.ufl.edu/ccmtdna.html]. New 380 bp sequences will continue to be named in the order that they are reported.

2. The most common variant or the first variant of the longer sequence for a 380 bp foundation sequence will be given the suffix “.1” following the foundation sequence name. For example, the most common long sequence for the foundation sequence CC-A1 will be given the designation CC-A1.1. Additional long-sequence variants for the foundation sequence will be designated with the suffix “.2”, “.3”, etc. yielding, for example, sequence designations CC-A1.2 and CC-A1.3.

3. If we have only one longer sequence for a 380 bp foundation sequence, that sequence will be given the suffix “.1”.

To facilitate haplotype designations and to avoid confusion among ocean basins, we are using the nomenclature of CC-A# (prefix A before the number is used to designate that it is from the Atlantic basin; P will be used for the Pacific).

If you have a new sequence, please email the new sequence to ACCSTR (accstr@zoology.ufl.edu), and we will confirm the status of the sequence and assign a sequence designation number. It is the responsibility of the author of the new sequence to submit the sequence to GenBank (http://ncbi.nlm.nih.gov). The data in GenBank are simultaneously made available to EMBL in Europe and the DNA Data Bank of Japan.

References:

Abreu-Grobois, A., J. Horrocks, A. Formia, P. Dutton, R. LeRoux, X. Velez-Zuazo, L. Soares, and P. Meylan. 2006. New mtDNA Dloop primers which work for a variety of marine turtle species may increase the resolution of mixed stock analyses. Book of Abstracts, 26th Annual Symposium on Sea Turtle Biology and Conservation, Crete, Greece.

Lopez-Jurado, L.F., C. Monzon-Arguello, E. Naro-Maciel, A. Marco, and C. Rico. 2007. Genetic structure of North Atlantic loggerhead sea turtles: insights from expanded mitochondrial analyses. 27th Annual Symposium on Sea Turtle Biology and Conservation, Myrtle Beach, SC, USA.

Monzon-Arguello, C., C. Rico, E. Naro-Maciel, N. Varo-Cruz, P. Lopez, A. Marco, and L.F. Lopez-Jurado. 2007. Cape Verde Islands: population genetic analysis of the loggerhead sea turtle. 27th Annual Symposium on Sea Turtle Biology and Conservation, Myrtle Beach, SC, USA.

Haplotype	Source
CC-A1.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu E. Naro-Maciel: enmaciel@amnh.org C. Monzon: catyma21@hotmail.com
CC-A1.2	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A1.3	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A1.4	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A1.5	C. Monzon: catyma21@hotmail.com
CC-A1.6	L. Garofalo: luisa.garofalo@uniroma2.it
CC-A1.7	B. Shamblin: brianshm@uga.edu
CC-A1.8	B. Shamblin: brianshm@uga.edu
CC-A2.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A2.2	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A2.3	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A2.4	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A2.5	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A2.6	P. Dutton: Peter.Dutton@noaa.gov
CC-A2.7	A. Bolten: ABB@zoology.ufl.edu
CC-A2.8	L. Garofalo: luisa.garofalo@uniroma2.it
CC-A2.9	L. Garofalo: luisa.garofalo@uniroma2.it
CC-A2.10	LaCasella, Frey, & Dutton: peter.dutton@noaa.gov
CC-A2.11	B. Shamblin: brianshm@uga.edu
CC-A3.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A3.2	O. Turkozan: oguz.turkozan@gmail.com
CC-A4.1	P. Dutton: Peter.Dutton@noaa.gov
CC-A4.2	C. Monzon: catyma21@hotmail.com
CC-A5.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-6.1	O. Turkozan, MEDASSSET: oguz.turkozan@gmail.com L. Garofalo: luisa.garofalo@uniroma2.it
CC-A7.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A7.2	P. Dutton: Peter.Dutton@noaa.gov
CC-A8.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A9.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A10.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A10.2	Original author(s) have withdrawn this haplotype sequence because of an error in the sequence submitted to ACCSTR. This haplotype designation has been removed from the database and will not be assigned to other sequences to avoid confusion.
CC-A10.3	A. Bolten: ABB@zoology.ufl.edu
CC-A10.4	O. Turkozan, MEDASSSET: oguz.turkozan@gmail.com
CC-A11.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A11.2	C. Monzon: catyma21@hotmail.com
CC-A11.3	J.T. Nielsen: jnielsen@bio.miami.edu
CC-A11.4	LaCasella, Frey, & Dutton: peter.dutton@noaa.gov
CC-A11.5	J.T. Nielsen: jnielsen@bio.miami.edu
CC-A12.1	J.T. Nielsen: jnielsen@bio.miami.edu
CC-A13.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A14.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A15.1	P. Dutton: Peter.Dutton@noaa.gov
CC-A17.1	A. Bolten: ABB@zoology.ufl.edu C. Monzon: catyma21@hotmail.com
CC-A17.2	C. Monzon: catyma21@hotmail.com
CC-A18.1	A. Bolten: ABB@zoology.ufl.edu
CC-A20.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A21.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A24.1	L. Soares: lsoares@ufl.edu
CC-A26.1	C. Carreras & M. Clusa: carlos_c_h@hotmail.com F. Maffucci: maffucci@szn.it
CC-A27.1	P. Dutton: Peter.Dutton@noaa.gov
CC-A28.1	L. Garofalo: luisa.garofalo@uniroma2.it
CC-A29.1	C. Carreras & M. Clusa: carlos_c_h@hotmail.com
CC-A31.1	L. Garofalo: luisa.garofalo@uniroma2.it
CC-A32.1	C. Carreras & M. Clusa: carlos_c_h@hotmail.com L. Garofalo: luisa.garofalo@uniroma2.it
CC-A36.1	P.Dutton: Peter.Dutton@noaa.gov A. Bolten: ABB@zoology.ufl.edu
CC-A36.2	J.T. Nielsen: jnielsen@bio.miami.edu
CC-A41.1	P. Dutton: Peter.Dutton@noaa.gov
CC-A42.1	J.T. Nielsen: jnielsen@bio.miami.edu
CC-A43.1	B. Shamblin: brianshm@uga.edu
CC-A44.1	P. Dutton: Peter.Dutton@noaa.gov
CC-A47.1	C. Monzon: catyma21@hotmail.com
CC-A49.1	P. Dutton: Peter.Dutton@noaa.gov
CC-A50.1	C. Carreras & M. Clusa: carlos_c_h@hotmail.com
CC-A51.1	B. Shamblin: brianshm@uga.edu
CC-A52.1	O. Turkozan: oguz.turkozan@gmail.com
CC-A53.1	O. Turkozan: oguz.turkozan@gmail.com
CC-A54.1	Original author(s) have withdrawn this haplotype sequence because of an error in the sequence submitted to ACCSTR. This haplotype designation has been removed from the database and will not be assigned to other sequences to avoid confusion.
CC-A59.1	J.T. Nielsen: jnielsen@bio.miami.edu
CC-A60.1	J.T. Nielsen: jnielsen@bio.miami.edu
CC-A61.1	LaCasella, Frey, & Dutton: peter.dutton@noaa.gov
CC-A62.1	LaCasella, Frey, & Dutton: peter.dutton@noaa.gov
CC-A63.1	C. Monzon: catyma21@hotmail.com
CC-A64.1	C. Monzon: catyma21@hotmail.com
CC-A65.1	C. Carreras & M. Clusa: carlos_c_h@hotmail.com
CC-A66.1	L. Garofalo: luisa.garofalo@uniroma2.it
CC-A67.1	L.V. Hurtado Gomez: lei_honey4@hotmail.com
CC-A68.1	F. Maffucci: maffucci@szn.it

Please note, the following sequences have not yet been trimmed to a consistent length.

CC-A1.1

AAGGGTTCAAACCTTCATCTCCGGTCCCCAAAACCGGAATCTTCCAATTAAACTACCCTTTGACGCAAAAGAAGCGCCAA

CATGTAAATTTACCTATATTCTCTGCCGTGCCCAACAGAACAATATCCGTAATACCTATCTATGTATTATCGTACATCAA

CTTATTTACCACTAGCATATGATCAGTAATGTTGTCGATTAATTTGGCTTTAAACATAAAAATTTATTAATTTTACATAA

ACTGTTTTAGTTACATGACTATTATACAGGTAATAAGAATGAAATGATATAGGACATAAAATTAAACCATTATTCTCAAC

CATGAATATCGTCGCAGTAATAGGTTATTTCTTAGTTCAGCTCATCACGAGAAATAAGCAACCCTTGTTAGTAAGATACA

ACATTACCAGTTTCAGGCCCATTAAGTCATATCGTACATAACTGATCTATTCTGGCCTCTGGTTG-TTTTTTCAGGCACA

TTAAGATAATAAAGTTCACTCGTTCCTCTTTAAAAGGCCTCTGGTT------AAATGAGTTCTATACATTAAATTTATAA

CCTGGCATACGGTGGTTTTACTTGCATATAGTAGTCTTTTTTTTCTCTTTGTGTTCTCAGGCCCGCATAACTGATACCTG

CCAGATTAATGAGACTGGACCTACGTTCAAAATGATTGGTCGTGCAGAATATTTAATGGTGTTATTTAGTTAATGCTTTT

AGGACATATATTTTTATAAAAACTCACAACAGTTATTCACAAGCTAAAACCCATTACAACCATACTTTTTAGTTAAACCC

CCCC-ACCCCCATAAAC

CC-A1.2