http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971248
MITOGENOME ANNOUNCEMENT
Characterization of the mitogenome of Uropsilus gracilis and species delimitation Quanfen Hou1*, Feiyun Tu2*, Yang Liu1, and Shaoying Liu1 Sichuan Academy of Forestry, Chengdu, People’s Republic of China and 2Jiangxi Academy of Forestry, Nanchang, People’s Republic of China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 01/03/15 For personal use only.
1
Abstract
Keywords
The species diversity within the genus Uropsilus were underestimated: 10 species among the genus Uropsilus have been proposed. In this study, the complete mitochondrial genome of U. gracilis, with the topotype, was determined. It is 16,536 bp in length, comprising of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. The composition and arrangement of its genes are similar to most other mammals. The total base composition of the mitogenome is A, 33.4%; T, 30.3%; C, 22.7% and G, 13.6%, with a rich content of A+T pattern. We performed the similarity comparison based on 13 PCGs of three species of Asiatic shrew-like mole, U. gracilis, U. sp. 1 and U. soricipes. Pairwise sequence alignment showed that similarity data of U. gracilis versus U. sorcipes are significantly higher than those of U. gracilis versus U. sp.1. This pointed toward a cryptic species (U. sp.1) from Jiajin Mountains rather than U. gracilis.
Cryptic species, mitochondrial genome, species delimitation, Uropsilus gracilis
The Asiatic shrew-like moles are terrestrial species, distributed almost entirely in southwestern China (Wan et al., 2013). There are 10 recognized species within the genus Uropsilus: U. aequodonenia, U. andersoni, U. atronates, U. gracilis, U. investigator, U. nivatus, U. sorcipes, U. sp. 1, U. sp. 2 and U. sp. 3 (Liu et al., 2013; Wan et al., 2013). However, the mitogenome data (Tu et al., 2014a) of only five species (U. aequodonenia, U. andersoni, U. nivatus, U. sorcipes and U. sp. 1) have been reported. SAF_JJSA109, sampling from Jiajin Mountains, was first identified as U. gracilis (Tu et al., 2012). Recently, Tu et al. (2014a) based on Cytb genes constructed the phylogenetic tree following the study of Wan et al. (2013) and reconsidered the specimen as U. sp. 1. In the present study, we determined the complete mitochondrial genome of U. gracilis (16,536 bp; GenBank Accession No. KM379136), with the topotype SAF_NC0403, Jinfo Mountains, Nanchuan, Chongqing (latitude: 29.028 N, longitude: 107.187 E), to further confirm the species status of U. sp. 1. To perform the similarity comparison using pairwise sequence alignment (PSA), we retrieved 13 protein-coding genes (PCGs) (ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, ND6, Cytb) of two species: U. sp. 1 (JX034737), U. soricipes (JQ658979) using GenScalpel v1.0 (Yin et al., 2012), and combing 13 protein-coding genes of U. gracilis determined in this study. Based on the 13 protein-coding genes, we performed the PSA analysis between U. gracilis versus U. soricipes and U. gracilis versus U. sp. 1 using EMBOSS Needle online platform
History Received 3 September 2014 Accepted 19 September 2014 Published online 20 October 2014
(http://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html). To compare the significant level of the two data (U. gracilis versus U. soricipes, U. gracilis versus U. soricipes), independent samples t-test was carried out using SPSS17.0 statistic software (SPSS, Chicago, IL). The composition and arrangement of the mitochondrial genome of U. gracilis are similar to those of other mammal Table 1. Comparison of sequence similarity based on the mitochondrial 13 protein-coding genes. Similarity/% Protein-coding genes ND1 ND2 COX1 COX2 ATP8 ATP6 COX3 ND3 ND4L ND4 ND5 ND6 Cytb
U. gracilis versus U. sp.1
U. gracilis versus U. soricipes
86.1 85.1 86.9 88.6 93.6 89.1 87.4 87.3 85.5 84.9 85.4 86.4 86.7
92.1 90.4 92.4 91.8 95.1 92.2 92.5 90.5 90.6 92.1 90.9 91.9 91.6
t-test: t ¼ 6.460, p50.001.
*These two authors contributed equally to this work. Correspondence: Shaoying Liu, Sichuan Academy of Forestry, Chengdu 610081, People’s Republic of China. Tel: + 86 28 83226632. Fax: +86 28 83222080. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 01/03/15 For personal use only.
2
Q. Hou et al.
Mitochondrial DNA, Early Online: 1–2
mitochondrial genomes, including 13 PCGs, 22 tRNA genes, 2 rRNA genes and a putative control region (Supporting Information, Table S1). The entire mitochondrial base composition is A, 33.4%; T, 30.3%; C, 22.7% and G, 13.6%, with an (A+T)-rich pattern of mammal mitochondrial genomes (Tu et al., 2014b). The similarity data are provided in Table 1. The similarity data of U. gracilis versus U. soricipes are significantly higher than those of U. gracilis versus U. sp. 1 (Table 1, t ¼ 6.460, p50.001). Combining with the PSA analysis, we further implied that SAF_JJSA109 is a cryptic species, U. sp. 1, in concordant with the previous studies (Tu et al., 2014a; Wan et al., 2013). Many methods such as genetic distance analysis, phylogenetic tree, DNA barcoding, are commonly used for species delimitation. The method based on similarity using PSA in this study, might be an extra example for species delimitation. The mitogenome of U. gracilis determined based on the topotype will be a very useful for taxonomy and systematics. More mitogenomic data are required to better elucidate the phylogenetic relationships within the genus Uropsilus.
Acknowledgements We would like to acknowledge Dr. Yu Xu at Pingdingshan University for statistic analysis. We are also very grateful to Dr. Zhenxin Fan at Sichuan University for his great efforts to correct English language errors in the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was funded by the National Natural Science Foundation of China (31272274).
References Liu Y, Liu SY, Sun ZY, Guo P, Fan ZX, Murphy RW. (2013). A new species of Uropsilus (Talpidae: Uropsilinae) from Sichuan, China. Acta Theriol Sin 33:113-22 (in Chinese). Tu FY, Fan ZX, Chen SD, Yin YH, Li P, Zhang XY, Liu SY, Yue BS. (2012). The complete mitochondrial genome sequence of the Gracile shrew mole, Uropsilus gracilis (Soricomorpha: Talpidae). Mitochondr DNA 23:382–4. Tu FY, Fan ZX, Murphy RW, Chen SD, Zhang XY, Yan CC, Liu Y, et al. (2014a). Molecular phylogenetic relationships among Asiatic shrew moles inferred from the complete mitogenomes. J Zool Syst Evol Res DOI: 10.1111/jzs.12081. Tu FY, Liu SY, Liu Y, Sun ZY, Yin YH, Yan CC, Lu L,Yue BS, Zhang XY. (2014b). Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne-Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China). J Nat Hist 48: 1467–83. Wan T, He K, Jiang XL. (2013). Multilocus phylogeny and cryptic diversity in Asian shrew-like moles (Uropsilus, Talpidae): implications for taxonomy and conservation. BMC Evol Biol 13:232. Yin YH, Du LM, Yue BS. (2012). GenScalpel: An application for sequence retrieval and extraction from the GenBank flatfile. J Hered 103:908–11.
Supplementary material available online Supplementary Table S1
MITOGENOME ANNOUNCEMENT
Characterization of the mitogenome of Uropsilus gracilis and species delimitation Quanfen Hou1*, Feiyun Tu2*, Yang Liu1, and Shaoying Liu1 Sichuan Academy of Forestry, Chengdu, People’s Republic of China and 2Jiangxi Academy of Forestry, Nanchang, People’s Republic of China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 01/03/15 For personal use only.
1
Abstract
Keywords
The species diversity within the genus Uropsilus were underestimated: 10 species among the genus Uropsilus have been proposed. In this study, the complete mitochondrial genome of U. gracilis, with the topotype, was determined. It is 16,536 bp in length, comprising of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. The composition and arrangement of its genes are similar to most other mammals. The total base composition of the mitogenome is A, 33.4%; T, 30.3%; C, 22.7% and G, 13.6%, with a rich content of A+T pattern. We performed the similarity comparison based on 13 PCGs of three species of Asiatic shrew-like mole, U. gracilis, U. sp. 1 and U. soricipes. Pairwise sequence alignment showed that similarity data of U. gracilis versus U. sorcipes are significantly higher than those of U. gracilis versus U. sp.1. This pointed toward a cryptic species (U. sp.1) from Jiajin Mountains rather than U. gracilis.
Cryptic species, mitochondrial genome, species delimitation, Uropsilus gracilis
The Asiatic shrew-like moles are terrestrial species, distributed almost entirely in southwestern China (Wan et al., 2013). There are 10 recognized species within the genus Uropsilus: U. aequodonenia, U. andersoni, U. atronates, U. gracilis, U. investigator, U. nivatus, U. sorcipes, U. sp. 1, U. sp. 2 and U. sp. 3 (Liu et al., 2013; Wan et al., 2013). However, the mitogenome data (Tu et al., 2014a) of only five species (U. aequodonenia, U. andersoni, U. nivatus, U. sorcipes and U. sp. 1) have been reported. SAF_JJSA109, sampling from Jiajin Mountains, was first identified as U. gracilis (Tu et al., 2012). Recently, Tu et al. (2014a) based on Cytb genes constructed the phylogenetic tree following the study of Wan et al. (2013) and reconsidered the specimen as U. sp. 1. In the present study, we determined the complete mitochondrial genome of U. gracilis (16,536 bp; GenBank Accession No. KM379136), with the topotype SAF_NC0403, Jinfo Mountains, Nanchuan, Chongqing (latitude: 29.028 N, longitude: 107.187 E), to further confirm the species status of U. sp. 1. To perform the similarity comparison using pairwise sequence alignment (PSA), we retrieved 13 protein-coding genes (PCGs) (ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, ND6, Cytb) of two species: U. sp. 1 (JX034737), U. soricipes (JQ658979) using GenScalpel v1.0 (Yin et al., 2012), and combing 13 protein-coding genes of U. gracilis determined in this study. Based on the 13 protein-coding genes, we performed the PSA analysis between U. gracilis versus U. soricipes and U. gracilis versus U. sp. 1 using EMBOSS Needle online platform
History Received 3 September 2014 Accepted 19 September 2014 Published online 20 October 2014
(http://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html). To compare the significant level of the two data (U. gracilis versus U. soricipes, U. gracilis versus U. soricipes), independent samples t-test was carried out using SPSS17.0 statistic software (SPSS, Chicago, IL). The composition and arrangement of the mitochondrial genome of U. gracilis are similar to those of other mammal Table 1. Comparison of sequence similarity based on the mitochondrial 13 protein-coding genes. Similarity/% Protein-coding genes ND1 ND2 COX1 COX2 ATP8 ATP6 COX3 ND3 ND4L ND4 ND5 ND6 Cytb
U. gracilis versus U. sp.1
U. gracilis versus U. soricipes
86.1 85.1 86.9 88.6 93.6 89.1 87.4 87.3 85.5 84.9 85.4 86.4 86.7
92.1 90.4 92.4 91.8 95.1 92.2 92.5 90.5 90.6 92.1 90.9 91.9 91.6
t-test: t ¼ 6.460, p50.001.
*These two authors contributed equally to this work. Correspondence: Shaoying Liu, Sichuan Academy of Forestry, Chengdu 610081, People’s Republic of China. Tel: + 86 28 83226632. Fax: +86 28 83222080. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 01/03/15 For personal use only.
2
Q. Hou et al.
Mitochondrial DNA, Early Online: 1–2
mitochondrial genomes, including 13 PCGs, 22 tRNA genes, 2 rRNA genes and a putative control region (Supporting Information, Table S1). The entire mitochondrial base composition is A, 33.4%; T, 30.3%; C, 22.7% and G, 13.6%, with an (A+T)-rich pattern of mammal mitochondrial genomes (Tu et al., 2014b). The similarity data are provided in Table 1. The similarity data of U. gracilis versus U. soricipes are significantly higher than those of U. gracilis versus U. sp. 1 (Table 1, t ¼ 6.460, p50.001). Combining with the PSA analysis, we further implied that SAF_JJSA109 is a cryptic species, U. sp. 1, in concordant with the previous studies (Tu et al., 2014a; Wan et al., 2013). Many methods such as genetic distance analysis, phylogenetic tree, DNA barcoding, are commonly used for species delimitation. The method based on similarity using PSA in this study, might be an extra example for species delimitation. The mitogenome of U. gracilis determined based on the topotype will be a very useful for taxonomy and systematics. More mitogenomic data are required to better elucidate the phylogenetic relationships within the genus Uropsilus.
Acknowledgements We would like to acknowledge Dr. Yu Xu at Pingdingshan University for statistic analysis. We are also very grateful to Dr. Zhenxin Fan at Sichuan University for his great efforts to correct English language errors in the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was funded by the National Natural Science Foundation of China (31272274).
References Liu Y, Liu SY, Sun ZY, Guo P, Fan ZX, Murphy RW. (2013). A new species of Uropsilus (Talpidae: Uropsilinae) from Sichuan, China. Acta Theriol Sin 33:113-22 (in Chinese). Tu FY, Fan ZX, Chen SD, Yin YH, Li P, Zhang XY, Liu SY, Yue BS. (2012). The complete mitochondrial genome sequence of the Gracile shrew mole, Uropsilus gracilis (Soricomorpha: Talpidae). Mitochondr DNA 23:382–4. Tu FY, Fan ZX, Murphy RW, Chen SD, Zhang XY, Yan CC, Liu Y, et al. (2014a). Molecular phylogenetic relationships among Asiatic shrew moles inferred from the complete mitogenomes. J Zool Syst Evol Res DOI: 10.1111/jzs.12081. Tu FY, Liu SY, Liu Y, Sun ZY, Yin YH, Yan CC, Lu L,Yue BS, Zhang XY. (2014b). Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne-Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China). J Nat Hist 48: 1467–83. Wan T, He K, Jiang XL. (2013). Multilocus phylogeny and cryptic diversity in Asian shrew-like moles (Uropsilus, Talpidae): implications for taxonomy and conservation. BMC Evol Biol 13:232. Yin YH, Du LM, Yue BS. (2012). GenScalpel: An application for sequence retrieval and extraction from the GenBank flatfile. J Hered 103:908–11.
Supplementary material available online Supplementary Table S1
