http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003826
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the black-tailed brush lizard Urosaurus nigricaudus (Reptilia, Squamata, Phrynosomatidae) Pedro Henrique Bernardo1, Eduardo Felipe Aguilera-Miller2, Sergio Ticul A´lvarez-Castan˜eda2, Fausto Roberto Me´ndez-de la Cruz3, and Robert W. Murphy1,4
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 04/21/15 For personal use only.
1
Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, 2Centro de Investigaciones Biolo´gicas del Noroeste, La Paz, Baja California Sur, Me´xico, 3Laboratorio de Herpetologı´a, Instituto de Biologı´a, Universidad Nacional Auto´noma de Me´xico, Me´xico, DF, Mexico, and 4Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
Abstract
Keywords
Previous studies using mitochondrial DNA (mtDNA) genes suggest the black-tailed brush lizard, Urosaurus nigricaudus, which is a small-sized lizard from the peninsula of Baja California, Mexico, has 4 deeply isolated mtDNA lineages with sequence divergence ranging from 4% to 11.2%. We present its complete mitochondrial genome. This genome is 17,298 bp long and comprises 2 rRNAs, 22 tRNAs, 13 protein-coding genes, 1 L-strand origin of replication and 1 control region. The overall nucleotide content is A ¼ 34.2%; C ¼ 26.8%; G ¼ 13.5%; T ¼ 25.5%. The gene organization and features agree with the general vertebrate organization and that found in other lizards. The control region is 1909 bp long and is located between tRNAPro and tRNAPhe.
Control region, genome organization, lizard, mitogenome
The black-tailed brush lizard, Urosaurus nigricaudus, is a small, diurnal and arboreal lizard endemic to the Baja California Peninsula, Mexico and Southern California, USA. A first study on its biogeography using CytB and APTase6 gene sequences found a deeply divergent mtDNA lineages differing from 4% to 11.2% of nucleotides (Lindell et al., 2008). As part of our efforts to understand the evolutionary implications of the parapatric
History Received 6 November 2014 Revised 26 November 2014 Accepted 5 December 2014 Published online 20 January 2015
mtDNA discordances, we sequenced the entire mitochondrial genome of this phrynosomatid lizard. The specimen sequenced was collected in the Oasis San Pedrito (62 km N of Cabo San Lucas), Baja California Sur, Mexico. Total DNA was extracted using the phenol-chloroform protocol (Sambrook et al., 1989). Polymerase chain reaction (PCR) amplifications were performed using universal mtDNA
Table 1. mtDNA genome organization and features in Urosaurus nigricaudus. Gene (Element) Phe
tRNA 12S tRNAVal 16S tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2
tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COI
Position 50 -30
Strand (H/L)
1–73 74–1014 1015–1083 1084–2611 2612–2686 2687–3655 3661–3731 3731–3800 3800–3869 3870–4902 4903–4979 4980–5048 5053–5125 5125–5157 5153–5218 5219–5289 5291–6838
H H H H H H H L H H H L L L L L H
Start codon
ATG
ATG
Stop codon
TAA
Space (+) Overlap ()
+3 1 1
Anticodon position
GAA
35–37
TAC
1046–1048
TAA
2647–2649
GAT TTG CAT
3692–3694 3767–3769 3831–3833
TCA TGC GTT
4935–4937 5016–5018 5090–5092
GCA GTA
5189–5191 5255–5257
T– +3 1 5
GTG
Anticodon
AGA
+1 5
(continued )
Correspondence: Pedro Henrique Bernardo, Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada. Tel: +1 (416) 586-8094. E-mail: [email protected]
2
P. H. Bernardo et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Gene (Element)
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 04/21/15 For personal use only.
Ser
tRNA tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CYTb tRNAThr tRNAPro CR
Position 50 -30
Strand (H/L)
6834–6904 6908–6975 6976–7663 7664–7731 7733–7900 7891–8573 8574–9357 9358–9427 9428–9773 9774–9841 9842–10,138 10,132–11,512 11,513–11,581 11,582–11,648 11,648–11,718 11,720–13,519 13,516–14,034 14,035–14,103 14,107–15,246 15,251–15,321 15,322–15,389 15,390–17,298
L H H H H H H H H H H H H H H H L L H H L
Start codon
Stop codon
ATG
T–
ATG ATG ATG
TAA TA– T–
ATG
T–
ATG ATG
TAA T–
ATG ATG
TAA TAA
ATG
TAA
primers for reptiles (Chen et al., 2005; Fu, 2000; Kocher et al., 1989; Leach & McGuirre, 2006; Nagy et al., 2012; Kumazawa & Endo, 2004). Specific primers for U. nigricaudus were developed to amplify the remaining parts of the genome and to assure all sequences overlapped before assembly. We used a 3730 DNA Analyzer (Applied Bio-Systems, Foster City, CA) to sequence all PCR products. The mitochondrial genome of the phrynosomatid Sceloporus occidentalis (Kumazawa & Endo, 2004, GeneBank Accession number AB079242) was used to assist the gene annotation. The complete mitochondrial genome of U. nigricaudus is 17,298 bp long (GenBank Accession No. KP091282). This genome has a typical vertebrate mitochondrial gene arrangement with 2 rRNAs, 22 tRNAs, 13 protein-coding genes and 1 control region (CR) (Table 1). The overall nucleotide content is A ¼ 34.2%; C ¼ 26.8%; G ¼ 13.5%; T ¼ 25.5%. Most of the genes are encoded on the H-strand except for ND6 and the tRNAs: tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro. All protein-coding genes start with ATG, except for COI (GTG). Stop codons are more variable. Seven genes present complete stop codon (TAA ¼ 6/13; AGA ¼ 1/13) and six genes have incomplete stop codons (TA– ¼ 1/13; T– – ¼ 5/13). The incomplete stop codons occur in genes that immediately precede a tRNA and are supposed to be completed with post-transcriptional polyadenilation (Ojala et al., 1981). A 33 bp fragment located in the WANCY cluster, between tRNAAsn and tRNACys, was considered the putative L-strand origin of replication. This mitochondrial genome presents eight regions with spacers and nine with overlaps. Uda (2011) suggested that overlapping could help to prevent rearrangements and loss of genes during replication of the mitochondrial genome. The CR is 1909 bp long and presents an arrangement typical of other vertebrates in having conserved regions (CSB1, CSB2 and CSB3) and an array of tandem repeats. These repeats are 37 bp long and are rich in G + C content. The CR region is located between tRNAPro and tRNAPhe. This complete mitochondrial genome will help to better understand the evolutionary process involved in the maintenance of the deep lineage discordances found on the peninsula of Baja California, Mexico. Further, it will facilitate more thorough analyses that rely on or include mitochondrial genes.
Space (+) Overlap ()
Anticodon
Anticodon position
+3
TGA GTC
6870–6872 6938–6940
+1 10
TTT
7694–7666
TCC
9389–9391
TCG
9804–9806
GTG GCT TAG
11,543–11,545 11,608–11,610 11,680–11,682
TTC
14,071–14,073
TGT TGG
15,284–15,286 15,364–15,362
7 1 +1 +4 +3 +4
Acknowledgements We thank Carmen Izmene Gutie´rrez-Rojas for the assistance during fieldwork and Amy Lathrop, Kristen Choffe, Oliver Haddrath, Tulio Soares, Cintya Segura-Trujillo and Griselda Gallegos Simental for assistance in the laboratory. Field equipment was generously donated by IDEA WILD.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article. This work was supported by Canada Graduate Scholarship from the National Science and Engineering Research Council of Canada (NSERC) to PHB, NSERC Discovery Grant A3148 to RWM, CONACYT 151189 to STAC and PAPIIT-UNAM 215011-3 to FRMC.
References Chen L, Murphy RW, Lathrop A, Ngo A, Orlov NL, Ho CT, Somorjai ILM. (2005). Taxonomic chaos in Asian ranid frogs: An initial phylogenetic resolution. Herpetol J 15:231–43. Fu J. (2000). Toward the phylogeny of the family Lacertidae – Why 4708 base pairs of mtDNA sequences cannot draw the picture. Biol J Linn Soc 71:203–17. Kocher TD, Thomas WK, Meyer A, Edwards SV, Pa¨a¨bo S, Villablanca FX, Wilson AC. (1989). Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86:6196–200. Kumazawa Y, Endo H (2004). Mitochondrial genome of the Komodo dragon: Efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Res 11:115–25. Leach AD, McGuire JA. (2006). Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: Evidence for a misleading mitochondrial gene tree. Mol Phylogenet Evol 39:628–44. Lindell J, Me´ndez de La Cruz FR, Murphy RW. (2008). Deep biogeographical history and cytonuclear discordance in the blacktailed brush lizard (Urosaurus nigricaudus) of Baja California. Biol J Linn Soc 94:89–104. Nagy ZT, Sonet G, Glaw F, Vences M. (2012). First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One 7: e34506.
DOI: 10.3109/19401736.2014.1003826
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 04/21/15 For personal use only.
Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Sambrook J, Fritsch EF, Maniatis T (1989). Molecular cloning—A laboratory manual, 2nd ed. New York, NY: Cold Spring Harbor Laboratory Press.
Mitogenome of U. nigricaudus
3
Uda K, Komeda Y, Koyama H, Koga K, Fujita T, Iwasaki N, Suzuki T. (2011). Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicus and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): Notable differences in gene arrangement. Gene 476:27–37.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the black-tailed brush lizard Urosaurus nigricaudus (Reptilia, Squamata, Phrynosomatidae) Pedro Henrique Bernardo1, Eduardo Felipe Aguilera-Miller2, Sergio Ticul A´lvarez-Castan˜eda2, Fausto Roberto Me´ndez-de la Cruz3, and Robert W. Murphy1,4
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 04/21/15 For personal use only.
1
Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, 2Centro de Investigaciones Biolo´gicas del Noroeste, La Paz, Baja California Sur, Me´xico, 3Laboratorio de Herpetologı´a, Instituto de Biologı´a, Universidad Nacional Auto´noma de Me´xico, Me´xico, DF, Mexico, and 4Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
Abstract
Keywords
Previous studies using mitochondrial DNA (mtDNA) genes suggest the black-tailed brush lizard, Urosaurus nigricaudus, which is a small-sized lizard from the peninsula of Baja California, Mexico, has 4 deeply isolated mtDNA lineages with sequence divergence ranging from 4% to 11.2%. We present its complete mitochondrial genome. This genome is 17,298 bp long and comprises 2 rRNAs, 22 tRNAs, 13 protein-coding genes, 1 L-strand origin of replication and 1 control region. The overall nucleotide content is A ¼ 34.2%; C ¼ 26.8%; G ¼ 13.5%; T ¼ 25.5%. The gene organization and features agree with the general vertebrate organization and that found in other lizards. The control region is 1909 bp long and is located between tRNAPro and tRNAPhe.
Control region, genome organization, lizard, mitogenome
The black-tailed brush lizard, Urosaurus nigricaudus, is a small, diurnal and arboreal lizard endemic to the Baja California Peninsula, Mexico and Southern California, USA. A first study on its biogeography using CytB and APTase6 gene sequences found a deeply divergent mtDNA lineages differing from 4% to 11.2% of nucleotides (Lindell et al., 2008). As part of our efforts to understand the evolutionary implications of the parapatric
History Received 6 November 2014 Revised 26 November 2014 Accepted 5 December 2014 Published online 20 January 2015
mtDNA discordances, we sequenced the entire mitochondrial genome of this phrynosomatid lizard. The specimen sequenced was collected in the Oasis San Pedrito (62 km N of Cabo San Lucas), Baja California Sur, Mexico. Total DNA was extracted using the phenol-chloroform protocol (Sambrook et al., 1989). Polymerase chain reaction (PCR) amplifications were performed using universal mtDNA
Table 1. mtDNA genome organization and features in Urosaurus nigricaudus. Gene (Element) Phe
tRNA 12S tRNAVal 16S tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2
tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COI
Position 50 -30
Strand (H/L)
1–73 74–1014 1015–1083 1084–2611 2612–2686 2687–3655 3661–3731 3731–3800 3800–3869 3870–4902 4903–4979 4980–5048 5053–5125 5125–5157 5153–5218 5219–5289 5291–6838
H H H H H H H L H H H L L L L L H
Start codon
ATG
ATG
Stop codon
TAA
Space (+) Overlap ()
+3 1 1
Anticodon position
GAA
35–37
TAC
1046–1048
TAA
2647–2649
GAT TTG CAT
3692–3694 3767–3769 3831–3833
TCA TGC GTT
4935–4937 5016–5018 5090–5092
GCA GTA
5189–5191 5255–5257
T– +3 1 5
GTG
Anticodon
AGA
+1 5
(continued )
Correspondence: Pedro Henrique Bernardo, Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada. Tel: +1 (416) 586-8094. E-mail: [email protected]
2
P. H. Bernardo et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Gene (Element)
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 04/21/15 For personal use only.
Ser
tRNA tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CYTb tRNAThr tRNAPro CR
Position 50 -30
Strand (H/L)
6834–6904 6908–6975 6976–7663 7664–7731 7733–7900 7891–8573 8574–9357 9358–9427 9428–9773 9774–9841 9842–10,138 10,132–11,512 11,513–11,581 11,582–11,648 11,648–11,718 11,720–13,519 13,516–14,034 14,035–14,103 14,107–15,246 15,251–15,321 15,322–15,389 15,390–17,298
L H H H H H H H H H H H H H H H L L H H L
Start codon
Stop codon
ATG
T–
ATG ATG ATG
TAA TA– T–
ATG
T–
ATG ATG
TAA T–
ATG ATG
TAA TAA
ATG
TAA
primers for reptiles (Chen et al., 2005; Fu, 2000; Kocher et al., 1989; Leach & McGuirre, 2006; Nagy et al., 2012; Kumazawa & Endo, 2004). Specific primers for U. nigricaudus were developed to amplify the remaining parts of the genome and to assure all sequences overlapped before assembly. We used a 3730 DNA Analyzer (Applied Bio-Systems, Foster City, CA) to sequence all PCR products. The mitochondrial genome of the phrynosomatid Sceloporus occidentalis (Kumazawa & Endo, 2004, GeneBank Accession number AB079242) was used to assist the gene annotation. The complete mitochondrial genome of U. nigricaudus is 17,298 bp long (GenBank Accession No. KP091282). This genome has a typical vertebrate mitochondrial gene arrangement with 2 rRNAs, 22 tRNAs, 13 protein-coding genes and 1 control region (CR) (Table 1). The overall nucleotide content is A ¼ 34.2%; C ¼ 26.8%; G ¼ 13.5%; T ¼ 25.5%. Most of the genes are encoded on the H-strand except for ND6 and the tRNAs: tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro. All protein-coding genes start with ATG, except for COI (GTG). Stop codons are more variable. Seven genes present complete stop codon (TAA ¼ 6/13; AGA ¼ 1/13) and six genes have incomplete stop codons (TA– ¼ 1/13; T– – ¼ 5/13). The incomplete stop codons occur in genes that immediately precede a tRNA and are supposed to be completed with post-transcriptional polyadenilation (Ojala et al., 1981). A 33 bp fragment located in the WANCY cluster, between tRNAAsn and tRNACys, was considered the putative L-strand origin of replication. This mitochondrial genome presents eight regions with spacers and nine with overlaps. Uda (2011) suggested that overlapping could help to prevent rearrangements and loss of genes during replication of the mitochondrial genome. The CR is 1909 bp long and presents an arrangement typical of other vertebrates in having conserved regions (CSB1, CSB2 and CSB3) and an array of tandem repeats. These repeats are 37 bp long and are rich in G + C content. The CR region is located between tRNAPro and tRNAPhe. This complete mitochondrial genome will help to better understand the evolutionary process involved in the maintenance of the deep lineage discordances found on the peninsula of Baja California, Mexico. Further, it will facilitate more thorough analyses that rely on or include mitochondrial genes.
Space (+) Overlap ()
Anticodon
Anticodon position
+3
TGA GTC
6870–6872 6938–6940
+1 10
TTT
7694–7666
TCC
9389–9391
TCG
9804–9806
GTG GCT TAG
11,543–11,545 11,608–11,610 11,680–11,682
TTC
14,071–14,073
TGT TGG
15,284–15,286 15,364–15,362
7 1 +1 +4 +3 +4
Acknowledgements We thank Carmen Izmene Gutie´rrez-Rojas for the assistance during fieldwork and Amy Lathrop, Kristen Choffe, Oliver Haddrath, Tulio Soares, Cintya Segura-Trujillo and Griselda Gallegos Simental for assistance in the laboratory. Field equipment was generously donated by IDEA WILD.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article. This work was supported by Canada Graduate Scholarship from the National Science and Engineering Research Council of Canada (NSERC) to PHB, NSERC Discovery Grant A3148 to RWM, CONACYT 151189 to STAC and PAPIIT-UNAM 215011-3 to FRMC.
References Chen L, Murphy RW, Lathrop A, Ngo A, Orlov NL, Ho CT, Somorjai ILM. (2005). Taxonomic chaos in Asian ranid frogs: An initial phylogenetic resolution. Herpetol J 15:231–43. Fu J. (2000). Toward the phylogeny of the family Lacertidae – Why 4708 base pairs of mtDNA sequences cannot draw the picture. Biol J Linn Soc 71:203–17. Kocher TD, Thomas WK, Meyer A, Edwards SV, Pa¨a¨bo S, Villablanca FX, Wilson AC. (1989). Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86:6196–200. Kumazawa Y, Endo H (2004). Mitochondrial genome of the Komodo dragon: Efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Res 11:115–25. Leach AD, McGuire JA. (2006). Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: Evidence for a misleading mitochondrial gene tree. Mol Phylogenet Evol 39:628–44. Lindell J, Me´ndez de La Cruz FR, Murphy RW. (2008). Deep biogeographical history and cytonuclear discordance in the blacktailed brush lizard (Urosaurus nigricaudus) of Baja California. Biol J Linn Soc 94:89–104. Nagy ZT, Sonet G, Glaw F, Vences M. (2012). First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One 7: e34506.
DOI: 10.3109/19401736.2014.1003826
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 04/21/15 For personal use only.
Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Sambrook J, Fritsch EF, Maniatis T (1989). Molecular cloning—A laboratory manual, 2nd ed. New York, NY: Cold Spring Harbor Laboratory Press.
Mitogenome of U. nigricaudus
3
Uda K, Komeda Y, Koyama H, Koga K, Fujita T, Iwasaki N, Suzuki T. (2011). Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicus and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): Notable differences in gene arrangement. Gene 476:27–37.
