Revised Reptile Mitochondrial Genome Annotations.
The following changes have been made to provide consistency in reptile mitochondrial gene/region
start and stop positions. * = encoded by the L strand.
Protein-Coding Genes
Alligator1 - COI ends at 6876 with an AGG stop codon (not >6867 with ‘TAT’).
Caiman
- ATPase8 ends at 7988 with a TAA stop codon (not 7974 with T--).
ASNTurtle - NADH1 ends at 3753 with a TAG stop codon (not 3752 with TA-).
- NADH2 ends at 5003 with a TAA stop codon (not 5002 with TA-).
- NADH6* starts at 14255 with a GTG start codon (not 14252 with ATA).
GreTurtle - NADH1 ends at 3771 with a TAG stop codon (not 3770 with TA-).
- NADH2 ends at 5018 with a TAG stop codon (not 5016 with T--).
- ATPase6 ends at 8682 with a TAA stop codon (not 8681 with TA-).
- NADH3 ends at 9885 with a TAG stop codon (not 9883 with T--).
MSSTurtle - NADH4L ends at 10267 with a TAA stop codon (not 10238 with T--).
Note: While position 10238 is the correct stop point based on alignment, whereas a
stop point at 10267 gives an extra 9 amino acids, this gene does not abut a tRNA and
thus an incomplete (T--) stop codon is not 'possible'.
- NADH6* starts at 14114 with a GTG start codon (not 14117 with ATG) i.e. directly
after the end of tRNA-Glu*, not overlapping with it.
BTMSkink - ATPase6 ends at 8570 with a TAA stop codon (not 8569 with TA-).
- NADH5 ends at 13550 with an AGG stop codon (not 13530 with T--).
Iguana
- ATPase6 ends at 8609 with a TAA stop codon (not 8607 with T--).
- NADH4L ends at 10174 with a TAA stop codon (not 10172 with T--).
Snake
- NADH2 ends at 5860 with a TAG stop codon (not 5858 with T--).
- NADH4L ends at 11062 with a TAA stop codon (not 11061 with TA-).
tRNAs
Alligator1 - tRNA-Ile starts at 3676 (not 3674) and ends at 3747 (not 3744).
- tRNA-Met ends at 3884 (not 3887).
- tRNA-Trp starts at 4951 (not 4950) and ends at 5024 (not 5025).
- tRNA-Ala* ends at 5028 (not 5030) and starts at 5096 (not 5095).
- tRNA-Tyr* starts at 5312 (not 5317).
- tRNA-Ser (UCN)* starts at 6942 (not 6945).
- tRNA-Asp starts at 6949 (not 6948) and ends at 7020 (not 7021).
- tRNA-Ser (AGY) ends at 11676 (not 11682).
- tRNA-His ends at 11756 (not 11755).
Supplementary Information 6: Revised Reptile Mt Genome Annotations, 3/3/16, page 1 of 6
- one nt (C) has been omitted from one of the anticodon stems in tRNA-Glu*
(Alligator2
has an extra C in this position, as did an earlier version of the Alligator1 sequence).
- tRNA-Thr starts at 15424 (not 15423) and ends at 15494 (not 15496).
- tRNA-Pro* ends at 15513 (not 15495).
Caiman
- tRNA-Ile starts at 3690 (not 3689).
- tRNA-Trp starts at 4959 (not 4958).
- tRNA-Ala* ends at 5037 (not 5039) and starts at 5105 (not 5104).
- tRNA-Asn* ends at 5107 (not 5108).
- tRNA-Tyr* starts at 5322 (not 5327).
- tRNA-Gly starts at 9425 (not 9424).
- tRNA-Arg ends at 9926 (not 9925).
- tRNA-Ser (AGY) starts at 11852 (not 11851) and ends at 11917 (not 11915).
- tRNA-Leu (CUN) starts at 11999 (not 11998) and ends at 12070 (not 12069).
- tRNA-Glu* ends at 14383 (not 14382) and starts at 14451 (not 14450).
- tRNA-Thr starts at 15684 (not 15686) and ends at 15756 (not 15757).
- tRNA-Pro* ends at 15762 (not 15758).
ASNTurtle - tRNA-Gln* ends at 3823 (not 3824) and starts at 3894 (not 3893).
- tRNA-His ends at 11655 (not 11656).
- tRNA-Ser (AGY) starts at 11656 (not 11658) and ends at 11715 (not 11714).
EPTurtle
- tRNA-Cys* starts at 5328 (not 5329).
- tRNA-Gly ends at 9536 (not 9535).
MSSTurtle - one nt (A) has been omitted from one of the DHU stems in tRNA-Asp.
- tRNA-Lys starts at 7767 (not 7768) and ends at 7839 (not 7838).
- two extra nt (both A) have been included in the DHU/anticodon loop of tRNA-His.
- one nt (probably A or G) has been omitted from either one of the acceptor stems or one
of the TC stems in tRNA-Pro*.
Iguana
- tRNA-Val starts at 1028 (not 1027) and ends at 1098 (not 1088).
- tRNA-Ile ends at 3772 (not 3771).
- tRNA-Gln* starts at 3840 (not 3839).
- tRNA-Asn* ends at 5089 (not 5098) and starts at 5161 (not 5170).
- tRNA-Cys* ends at 5188 (not 5189) and starts at 5253 (not 5252).
- tRNA-Ser (UCN)* ends at 6870 (not 6876) and starts at 6940 (not 6943).
Snake
- tRNA-Phe ends at 67 (not 65).
rRNAs
Alligator1 - 16S rRNA starts at 1045 (not 1046) i.e. directly after the end of tRNA-Val.
Alligator2 - 16S rRNA ends at 2423 (not 2432) i.e. directly before the start of tRNA-Leu (UUR).
Caiman
- 12S rRNA starts at 5 (not 1) based on 12S rRNA alignment.
- 16S rRNA starts at 1057 (not 1058) i.e. directly after the end of tRNA-Val.
Supplementary Information 6: Revised Reptile Mt Genome Annotations, 3/3/16, page 2 of 6
EPTurtle
- 16S rRNA starts at 1109 (not 1110) i.e. directly after the end of tRNA-Val.
Iguana
- 12S rRNA ends at 1027 (not 1026), because tRNA-Val starts at 1028 (not 1027).
- 16S rRNA starts at 1099 (not 1089, because tRNA-Val ends at 1098 (not 1088).
Snake
- 12S rRNA starts at 68 (not 66), because tRNA-Phe ends at 67 (not 65).
Control Region (CR) and Genome Length
Alligator1 - total length of genome = 16647 nt (not 16646 nt) because one nt has been omitted
from
tRNA-Glu*.
Caiman
- CR ends at 4 (not 17900), because 12S rRNA starts at 5 (not 1).
Snake
- CR ends at 17191 (not 17190) i.e. directly before the start of tRNA-Phe.
Supplementary Information 6: Revised Reptile Mt Genome Annotations, 3/3/16, page 3 of 6
Summary
Note: The missing nt in Alligator1’s tRNA-Glu and the missing/extra nt in MSSTurtle’s tRNAAsp,
tRNA-His and tRNA-Pro have not been included in the following statistics.
Discrepancies:
Protein-coding: 17 discrepancies affecting the start and end positions of 9 of the 13 genes
tRNAs:
53
‘’
‘’
‘’ ‘’ ‘’ ‘’
‘’
‘’ 21 ‘’ ‘’ 22 ‘’
rRNAs:
8
‘’
‘’
‘’ ‘’ ‘’ ‘’
‘’
‘’ both rRNAs
Control region: 2
‘’
‘’
‘’ end positions
Total: 78 discrepancies affecting 86% (32/37) of the genes plus 2 control region discrepancies.
Note: In the reptiles, only 9% (5/53) of the tRNA discrepancies involve tRNA-Ser (AGY).
Overall: 10.5 % (80/760) of start and end positions are affected overall
(= total # discrepancies/total # start and stop positions;
total # start and stop positions = # genes/regions (38) x 2 x # taxa (10) = 760).
Type of discrepancy:
1 nt
2 nt
3 nt
Prot-cod
6
5
2
tRNAs
32
8
4
rRNAs
4
1
CR
1
Total
43
1 nt:
2-3 nt:
>3 nt, ≤10 nt:
>10 nt:
4 nt
5 nt
6 nt
9 nt
10 nt
14 nt
1
1
2
2
1
18 nt
1
2
1
1
1
20 nt
29 nt
Total
1
1
17
1
53
8
1
14
6
3
2
2
2
4
2
1
1
1
1
80
54% (43/80)
25% (20/80)
16% (13/80)
5% (4/80)
Supplementary Information 6: Revised Reptile Mt Genome Annotations, 3/3/16, page 4 of 6
Note on Reptile Mitochondrial Genome Annotations.
We have accepted one unusual annotation and two exceptions to our guidelines for the
standardization of mitochondrial (mt) genome annotation (Slack et al. submitted, Materials and
Methods section). All involve reptile taxa and the Cytochrome b gene.
1. The start point of Cyt b in the African side-necked turtle (ASNTurtle).
One of our guidelines is ‘The start positions of protein-coding genes preceded by tRNAs are also
limited by the tRNA end points (no overlaps)’. Zardoya and Meyer (1998)’s annotation for the start
point of the ASNTurtle Cyt b gene gives an eight nucleotide (nt) overlap between the preceding
tRNA (tRNA-Glu) and the start of Cytb. Technically, this does not violate our guideline as tRNAGlu and Cytb are encoded by different strands of the mt genome (L and H respectively) and thus the
start rather than the end point of the tRNA is involved in the ‘overlap’. Nevertheless, it is unusual
(the other reptiles have an intergenic spacer of one-nine nt between tRNA-Glu and Cyt b). The
suggested start point appears to be correct based on an alignment of vertebrate Cytb sequences.
Furthermore, the next possible start codon for the ASNTurtle Cytb gene is 39 nt downstream and
would give a 367 aa protein (the other reptiles have 372-386 aa) and a long intergenic spacer (31 nt)
between tRNA-Glu/Cytb. We have therefore accepted Zardoya and Meyer (1998)’s annotation.
2. The stop codons of the alligator and caiman Cyt b genes.
Another of our guidelines is ‘With protein-coding genes followed by tRNAs, if there is a complete
stop codon preceding the tRNA this is accepted. If not, there are two possibilities: an incomplete (T
or TA) stop codon immediately adjacent to the start of the tRNA (completed by post-transcriptional
polyadenylation; Ojala et al., 1981) or a full stop codon plus a slight overlap with the tRNA’. Janke
and Arnason (1997), Mindell et al. (1999) and Janke et al. (2001)’s annotations for the alligator and
caiman Cytb stop codons involve incomplete (T) stop codons which are not immediately adjacent to
the start of the following tRNA (33 nt earlier in the alligator and 74 nt earlier in the caiman).
However, there is no possible incomplete (T or TA) stop codon adjacent to the start of tRNA-Thr in
these taxa. Moreover, accepting the first complete stop codon would give an unrealistically long
protein (408 aa in the alligator and 410 aa in the caiman, compared to 372-381 aa in the other
reptiles) and a long overlap with tRNA-Thr (36 nt in the alligator, 10 nt in the caiman). We have
thus accepted Janke and Arnason (1997), Mindell et al. (1999) and Janke et al. (2001)’s
annotations, despite their constituting an exception to our guidelines. Experimental research is
required in order to determine where exactly the functional endpoint of this gene is in crocodilians.
References.
Janke A. & Árnason Ú. (1997). The complete mitochondrial genome of Alligator mississippiensis
and the separation between recent Archosauria (birds and crocodiles). Mol. Biol. Evol. 14:
1266-1272.
Janke, A., Erpenbeck, D., Nilsson, M. & Árnason Ú. (2001). The mitochondrial genomes of the
iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote
phylogeny. Proc. R. Soc. Lond. B, Biol. Sci. 268: 623-631.
Mindell D. P., Sorenson M. D., Dimcheff D. E., Hasegawa M., Ast J. C. & Yuri T. (1999). Interordinal
relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48:
138-152.
Supplementary Information 6: Revised Reptile Mt Genome Annotations, 3/3/16, page 5 of 6
Ojala, D., Montoya, J. & Attardi, G. (1981). tRNA punctuation model of RNA processing in human
mitochondria. Nature 290: 470-474.
Slack, K. E., Janke, A., Penny, D. & Arnason, U. (submitted 2002 Gene). Two new avian
mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic
features.
Zardoya, R. & Meyer, A. (1998). Complete mitochondrial genome suggests diapsid affinities of
turtles. Proc. Natl. Acad. Sci. U.S.A. 95: 14226-14231.
Supplementary Information 6: Revised Reptile Mt Genome Annotations, 3/3/16, page 6 of 6