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Open Access Highly Accessed Research article

Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes

Robert W Meredith12, John Gatesy1 and Mark S Springer1*

Author Affiliations

1 Department of Biology, University of California, Riverside, CA 92521, USA

2 Current address: Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ, 07043, USA

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BMC Evolutionary Biology 2013, 13:20  doi:10.1186/1471-2148-13-20

Published: 23 January 2013

Additional files

Additional file 1:

Nexus alignment of ENAM exon 9 sequences for two crocodylians, one testudine, and five birds. The stop codon in crocodylians and Chrysemys picta occurs at positions 3788–3790. A 406 bp deletion that is shared by all five birds occurs near the 3’ end of the coding region at positions 3353–3758. Additional frameshift mutations are shared by four of five birds including representatives of Anseriformes, Galliformes, and Passeriformes (2634–2637). Cry SINE elements [47] in Chrysemys occur at positions 994–1138 and 4782–4994. Several long strings of Ns in Chrysemys picta were abridged to shorter strings of ten Ns.

Format: NEX Size: 91KB Download file

Open Data

Additional file 2:

Schematic alignment showing regions of ENAM exon 9 that were identified in Chrysemys picta. Green bars below sequence numbers show regions of sequence similarity between C. picta and Alligator mississippiensis. Red rectangles = frameshift mutations in C. picta; light blue rectangles = indels within the coding sequence that are in multiples of three base pairs; CRY = Cry SINE insertion; red arrow = position of stop codon in A. mississippiensis.

Format: PDF Size: 221KB Download file

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Open Data

Additional file 3:

Nexus alignment of AMBN exon sequences for two crocodylians, one testudine, and one bird. The start and stop codons in crocodylians occur at positions 127–129 (exon 2) and 1374–1376 (exon 11), respectively.

Format: NEX Size: 111KB Download file

Open Data

Additional file 4:

Schematic alignment showing regions of AMBN exons 1–11 that were identified in Chrysemys picta. Green bars below sequence numbers show regions of sequence similarity between C. picta and Alligator mississippiensis. Dark blue rectangles = numbered exons in A. mississippiensis; red rectangles = frameshift mutations in C. picta; light blue rectangles = indels within the coding sequence that are in multiples of three bp; dark blue arrow = position of start codon in A. mississippiensis; red arrow = position of stop codon in A. mississippiensis.

Format: PDF Size: 123KB Download file

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Open Data

Additional file 5:

Nexus alignment of AMBN exon sequences forHomo sapiens, Orycteropus aferand six other afrotherians, Dasypus novemcinctus, and Choloepus hoffmanni. The start and stop codons in Homo occur at positions 121–123 (exon 1) and 1468–1470 (exon 13), respectively. The presumed start codon in Dasypus occurs at positions 151–153. Dasypus shares the same stop codon as Homo at positions 1468–1470, whereas the presumed stop codon in Choloepus is at positions 1477–1479.

Format: NEX Size: 77KB Download file

Open Data

Additional file 6:

Nexus alignment of protein-coding AMBN sequences for 20 mammals that was used in selection analyses with PAML 4.5 [36].

Format: NEX Size: 43KB Download file

Open Data

Additional file 7:

Nexus alignment of AMEL exon sequences in nexus format for two crocodylians, two testudines, and five birds. The start and stop codons in crocodylians occur at positions 69–71 (exon 1) and 731–733 (exon 5), respectively. A putative one-bp frameshift deletion that is shared by all five birds species occurs at position 242 in exon 4.

Format: NEX Size: 49KB Download file

Open Data

Additional file 8:

Schematic alignment showing regions of AMEL exons 1–5 that were identified in Chrysemys picta and Pelodiscus sinensis . Bars below sequence numbers show regions of sequence similarity between Alligator mississippiensis and both testudines (green) or A. mississippiensis and one testudine (chartreuse). Dark blue rectangles = numbered exons in A. mississippiensis; red rectangles = frameshift mutations in C. picta; light blue rectangles = indels within the coding sequence that are in multiples of three bp; dark blue arrow = position of start codon in A. mississippiensis; red arrow = position of stop codon in A. mississippiensis.

Format: PDF Size: 63KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9:

Nexus alignment of Alligator mississippiensis AMEL exon 1 (positions 1–114), intron 1 (positions 115–813), and exon 2 (838–894) with exon 1 and flanking sequences from Chrysemys picta and Pelodiscus sinensis.

Format: NEX Size: 17KB Download file

Open Data

Additional file 10:

Nexus alignment of AMEL intron 4 (positions 1–662) and exon 5 (positions 663–844) sequences for Chrysemys picta and Pelodiscus sinensis.

Format: NEX Size: 11KB Download file

Open Data

Additional file 11:

Nexus alignment of AMEL sequences (exons 2–7) for Homo sapiens, Orycteropus afer and six other afrotherians (Echinops telfairi, Chrysochloris asiatica, Elephantulus edwardii, Trichechus manatus, Loxodonta africana, Procavia capensis), Dasypus novemcinctus, and Choloepus hoffmanni. The start and stop codons in Homo occur at positions 13–15 (exon 2) and 668–670 (exon 7), respectively. The mutated stop codon and frameshift mutation in exon 2 of Choloepus are clear in gnl|ti|1325289135 and gnl|ti|1311883086. The stop codon in exon 4 of Choloepus is confirmed by traces gnl|ti|1325336699 and gnl|ti|1312095734. The frameshift mutation in exon 6 of Choloepus is evident in trace gnl|ti|1363579107. The deletion that includes the 3’ region of intron 6 and first 14 bp of exon 7 in Dasypus is evident in gn|ti| 1886397515.

Format: NEX Size: 21KB Download file

Open Data