Research article
The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage
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* Corresponding author: Weiming Li liweim@msu.edu
1 Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
2 Research Technology Support Facility, Michigan State University, East Lansing, MI 48824, USA
3 The Monell Chemical Sense Center, 3500 Market Street, Philadelphia, PA 19104-3308, USA
BMC Evolutionary Biology 2009, 9:180 doi:10.1186/1471-2148-9-180
Published: 31 July 2009Additional files
Additional file 1:
Nucleic acid and peptide sequences of predicted intact single exon chemosensory receptors from the sea lamprey genome. Nucleotide and peptide sequences in FASTA format.
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Additional file 2:
NJ analysis of deuterostome CR genes. Neighbor-joining analysis including all intact lamprey OR and TAAR genes, representatives of Class I and II ORs from teleosts and tetrapods, and sea lamprey nearest-neighbor GLEAN-predicted chemosensory genes from the genome of the sea urchin Strongylocentrotus purpuratus. The urchin chemosensory genes form a single well-supported group whose position suggests a possible independent origin for echinoderm rhodopsin-type amine chemosensory receptors.
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Additional file 3:
NJ analysis of V1R from lamprey and representative gnathostomes. Neighbor-Joining analysis of putative lamprey V1R genes including teleosts and tetrapod representative V1Rs. Distances computed using the JTT matrix are included and statistical support in the unrooted tree is presented as a percentage of 1000 bootstraps.
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Additional file 4:
Lamprey and teleost V1R peptide sequence alignment. CLUSTALV Alignment of teleost V1R gene with lamprey V1R amino acid sequences. An alignment with a single teleost V1R (AAX10116) is included to emphasize the distant homologies in the V1R genes. Annotations from previous studies that allowed for the identification of putative V1R genes in Petromyzon are shown. Sites conserved in mouse V1Rs, N-linked glycosylation sites [22], and those sites differentially conserved in fish and mammal OR and V1r-like genes [7,23] are highlighted.
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Additional file 5:
NJ analysis of V2R, CASR and MGR from lamprey and representative gnathostomes. Neighbor-Joining analysis of V2R-, metabotropic glutamate- and calcium-sensing receptor amino acid sequences from sea lamprey and representative gnathostome taxa. Statistical support in the unrooted tree is represented by percentage of 1000 bootstrap replicates with distances computed by the JTT matrix method (MEGA). All positions containing gaps and missing data were eliminated from the dataset. 396 positions were analyzed in the final dataset.
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Additional file 6:
Identification of CRs expressed in the lamprey olfactory organ. Strategy used to identify the sea lamprey chemosensory receptor gene repertoire and to survey their expression in olfactory organ cDNA and NCBI EST databases.
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Additional file 7:
Supplemental Sequences from Niimura and Nei (2006) and Shi and Zhang (2007) used as queries for BLASTN, TBLASTN, PSI-BLAST searches and for the construction of position-specific scoring matrices (PSSMs). Complete list of nucleotide and amino acid sequences used to query the sea lamprey draft genome for potential chemosensory receptor genes.
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