The Complete Mitogenome of the Eurasian Blindsnake Xerotyphlops Vermicularis (Reptilia, Typhlopidae)

MITOCHONDRIAL DNA PART B 2019, VOL. 4, NO. 1, 1990–1991 https://doi.org/10.1080/23802359.2019.1617080

MITOGENOME ANNOUNCEMENT The complete mitogenome of the Eurasian blindsnake Xerotyphlops vermicularis (Reptilia, Typhlopidae)

Panagiotis Korniliosa,b,c aDepartment of Biology, University of Washington, Seattle, WA, USA; bThe Molecular Ecology Backshop, Loutraki, Greece; cInstitute of Evolutionary Biology, CSIC - Universitat Pompeu Fabra, Passeig Marıtim de la Barceloneta 37–49, Barcelona E-08003, Spain

ABSTRACT ARTICLE HISTORY The Eurasian or Greek blindsnake, Xerotyphlops vermicularis, is the only European representative of the Received 22 April 2019 infraorder Scolecophidia, a largely understudied group of snakes with a poor record of available mito- Accepted 3 May 2019 genomes. Its complete mitochondrial genome, the first reported for the genus Xerotyphlops,was KEYWORDS assembled through next-generation sequencing. Its total length is 16,568 bp and includes 22 tRNAs, 2 Xerotyphlops vermicularis; ribosomal RNA genes, 13 protein-coding genes, and a control region, showing the typical gene- Eurasian blindsnake; arrangement for Typhlopidae. Eight tRNAs and ND6 are encoded on the light strand, while all other mitogenome; mtDNA; genes are encoded on the heavy strand. Squamata; Typhlopidae

Snake are divided into two major infraorders, the ‘true ultraconserved elements (UCEs) under a sequence capture snakes’ Alethinophidia and the ‘wormsnakes’ Scolecophidia. protocol (Faircloth et al. 2012). The 150 bp paired-end library The latter are small to medium-sized burrowing snakes with was prepared using the Truseq Nano DNA kit (Illumina Inc., no external eyes that, despite their worldwide distribution San Diego, CA) and sequenced on a single Illumina HiSeq (except Antarctica) and their great number of species, they 4000 lane. The mitogenome was assembled de novo from have been very poorly studied (Nagy et al. 2015). Their the off-target sequences with NOVOPlasty 2.7.1 (Dierckxsens higher-level phylogenetics, systematics, and taxonomy have et al. 2017). Genes were annotated using the MITOS only recently been assessed (Adalsteinsson et al. 2009; Vidal WebServer (Bernt et al. 2013) and checked manually. et al. 2010; Kornilios et al. 2013; Hedges et al. 2014; Pyron Alignment with all available scolecophidian mitogenomes and Wallach 2014; Nagy et al. 2015; Miralles et al. 2018). They was done with MAFFT (Katoh et al. 2017). This dataset, after include more than 400 species and about 40 genera organ- removing the poorly aligned control region, was used to ized in five families: Anomalepididae, Gerrhopilidae, reconstruct a maximum-likelihood (ML) tree with IQ-TREE1.4.3 Typhlopidae, Leptotyphlopidae and Xenotyphlopidae (Uetz (Nguyen et al. 2015), using 1000 ultrafast bootstrap et al. 2019). alignments (Minh et al. 2013). The available mitochondrial genomes for Scolecophidia The Eurasian blindsnake’s mitogenome (Genbank acces- are very few. In fact, only five mitogenomes have been sion number MH745105) is 16,568 bp long and includes 22 sequenced, representing five species and genera and three of transfer RNA genes (duplicate tRNA-Leu and tRNA-Ser), 2 ribo- the families. Here I present the complete mitochondrial gen- somal RNA genes, 13 protein-coding genes, and a control ome of Xerotyphlops vermicularis Merrem, 1820, which is also region, showing the typical gene-arrangement for the first sequenced mitogenome of this genus, as a new add- Typhlopidae (type II in Qian et al. 2018). Eight tRNAs and ition to the poor existing record of wormsnake mitogenomes. ND6 are encoded on the light strand, while all others are Xerotyphlops vermicularis, known as the Eurasian or Greek encoded on the heavy strand. The overall composition of the blindsnake, belongs to Typhlopidae and is the only extant heavy strand is A (33.0%), T (27.7%), C (26.2%), and G scolecophidian representative occurring in Europe. It is most (13.1%). The ML mitogenomic phylogeny, rooted with the probably a species-complex (Kornilios et al. 2011, 2012; leptotyphlopid Rena humilis, is shown in Figure 1. Within the Kornilios 2017) and its type locality is ‘Greece’. An adult spe- monophyletic unit of Typhlopidae, Amerotyphlops represents cimen was collected in 2009 in Makri (Thrace, Greece; the South America group of typhlopids, while Xerotyphlops, 40.853932, 25.747042) and deposited in the Biology Indotyphlops, and Anilios represent the Asian one, as resulted Department, University of Patras (sample code TV071). Total in all contemporary DNA phylogenies (e.g. Miralles et al. genomic DNA was extracted and used, together with other 2018). The presented tree does not exhibit this phylogenetic squamate samples, in a comparative analysis that utilized configuration, but it is the very limited available

CONTACT Panagiotis Kornilios [email protected], [email protected] Institute of Evolutionary Biology, CSIC - Universitat Pompeu Fabra, Passeig Marıtim de la Barceloneta 37-49, E-08003 Barcelona, Spain ß 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MITOCHONDRIAL DNA PART B 1991

Figure 1. The maximum-likelihood tree based on the mitogenomes of Xerotyphlops vermicularis and all other available scolecophidians. Numbers next to nodes indicate bootstrap support values. scolecophidian mitogenomes and the overall representation Katoh K, Rozewicki J, Yamada KD. 2017. MAFFT online service: multiple gap that is responsible for this conflict. sequence alignment, interactive sequence choice and visualization. Brief Bioinform. bbx108. Kornilios P. 2017. Polytomies, signal and noise: revisiting the mitochon- Acknowledgements drial phylogeny and phylogeography of the Eurasian blindsnake species complex (Typhlopidae, Squamata). Zool Scr. 46:665–674. The sequence-capture work took place in the Leache Lab (Department of Kornilios P, Giokas S, Lymberakis P, Sindaco R. 2013. Phylogenetic pos- Biology, University of Washington). This work used the Vincent J. Coates ition, origin and biogeography of Palearctic and Socotran blind-snakes Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 (Serpentes: Typhlopidae). Mol Phylogenet Evol. 68:35–41. OD018174 Instrumentation Grant. Kornilios P, Ilgaz C¸, Kumlutas¸ Y, Giokas S, Fraguedakis-Tsolis S, Chondropoulos B. 2011. The role of Anatolian refugia in herpetofaunal Disclosure statement diversity: an mtDNA analysis of Typhlops vermicularis Merrem, 1820 (Squamata, Typhlopidae). Amphibia-Reptilia. 32:351–363. The author reports no conflicts of interest. The author alone is respon- Kornilios P, Ilgaz C¸, Kumlutas¸ Y, Lymberakis P, Moravec J, Sindaco R, sible for the content and writing of the paper. Rastegar-Pouyani N, Afroosheh M, Giokas S, Fraguedakis-Tsolis S, et al. 2012. Neogene climatic oscillations shape the biogeography and evolutionary history of the Eurasian blindsnake. Mol Phylogenet Evol. 62: Funding 856–873. Minh BQ, Nguyen MAT, von Haeseler A. 2013. Ultrafast approximation for This project has received funding from the European Union’s Horizon phylogenetic bootstrap. Mol Biol Evol. 30:1188–1195. 2020 research and innovation programme under the H2020 Marie Miralles A, Marin J, Markus D, Herrel A, Hedges SB, Vidal N. 2018. Skłodowska-Curie Actions [656006] (Project Acronym: CoPhyMed). Molecular evidence for the paraphyly of Scolecophidia and its evolutionary implications. J Evol Biol. 31:1782–1793. References Nagy ZT, Marion AB, Glaw F, Miralles A, Nopper J, Vences M, Hedges SB. 2015. Molecular systematics and undescribed diversity of Madagascan Adalsteinsson SA, Branch WR, Trape S, Vitt LJ, Hedges SB. 2009. scolecophidian snakes (Squamata: Serpentes). Zootaxa. 4040:31–47. Molecular phylogeny, classification, and biogeography of snakes of Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast the family Leptotyphlopidae (Reptilia, Squamata). Zootaxa. 2244:1–50. and effective stochastic algorithm for estimating maximum-likelihood € € Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, phylogenies. Mol Biol Evol. 32:268–274. Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan Pyron RA, Wallach V. 2014. Systematics of the blindsnakes (Serpentes: mitochondrial genome annotation. Mol Phylogenet Evol. 69:313–319. Scolecophidia: Typhlopoidea) based on molecular and morphological Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly evidence. Zootaxa. 3829:1–81. of organelle genomes from whole genome data. Nucleic Acids Res. Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. 2018. Multiple 45:e18. Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, independent structural dynamic events in the evolution of snake Glenn TC. 2012. Ultraconserved elements anchor thousands of genetic mitochondrial genomes. BMC Genomics. 1019:354. markers spanning multiple evolutionary timescales. Syst Biol. 61: Uetz P, Freed P, Hosek J. 2019. The Reptile Database; [accessed 2019 717–726. April 20]. http://www.reptile-database.org. Hedges SB, Marion AB, Lipp KM, Marin J, Vidal N. 2014. A taxonomic Vidal N, Marin J, Morini M, Donnellan S, Branch WR, Thomas R, Vences framework for typhlopid snakes from the Caribbean and other regions M, Wynn A, Cruaud C, Hedges SB. 2010. Blindsnake evolutionary tree (Reptilia, Squamata). Caribb Herpet. 49:1–61. reveals long history on Gondwana. Biol Lett. 6:558–561.