Dalton, Desire Lee

Du Plessis, Morne

Kotze, Antoinette

Smit-Robinson, Hanneline A.

English

The mitochondrial genome of Sarothrura ayresi was sequenced using next generation sequencing technology. The size of the genome is reported as 16,767 bp and comprises 13 protein-coding genes, 2rRNAs and 22 tRNAs. The organization of the genome is comparable to that of other bird species.A phylogenetic comparison mapped the relative relationship of Sarothrura ayresi with respect to otherspecies in the order Gruiformes

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Full Terms & Conditions of access and use can be found athttp://www.tandfonline.com/action/journalInformation?journalCode=tmdn20Download by: [196.21.229.2] Date: 24 April 2017, At: 23:54Mitochondrial DNA Part BResourcesISSN: (Print) 2380-2359 (Online) Journal homepage: http://www.tandfonline.com/loi/tmdn20Next generation sequencing yields themitochondrial genome of the critically endangeredSarothrura ayresi (white-winged flufftail)Morne Du Plessis, Desire L. Dalton, Hanneline A. Smit-Robinson &Antoinette KotzeTo cite this article: Morne Du Plessis, Desire L. Dalton, Hanneline A. Smit-Robinson & AntoinetteKotze (2017) Next generation sequencing yields the mitochondrial genome of the criticallyendangered Sarothrura ayresi (white-winged flufftail), Mitochondrial DNA Part B, 2:1, 236-237, DOI:10.1080/23802359.2017.1318675To link to this article:  http://dx.doi.org/10.1080/23802359.2017.1318675© 2017 The Author(s). Published by InformaUK Limited, trading as Taylor & FrancisGroup.Published online: 24 Apr 2017.Submit your article to this journal View related articles View Crossmark dataMITOGENOME ANNOUNCEMENTNext generation sequencing yields the mitochondrial genome of the criticallyendangered Sarothrura ayresi (white-winged flufftail)Morne Du Plessisa, Desire L. Daltona,b, Hanneline A. Smit-Robinsonc,d and Antoinette Kotzea,eaNational Zoological Gardens of South Africa, Pretoria, South Africa; bDepartment of Zoology, University of Venda, Thohoyandou, SouthAfrica; cBirdlLife South Africa, Parklands, Gauteng, South Africa; dApplied Behavioural Ecological & Ecosystem Research Unit (ABEERU), UNISA,Florida, South Africa; eGenetics Department, University of the Free State, Bloemfontein, South AfricaABSTRACTThe mitochondrial genome of Sarothrura ayresi was sequenced using next generation sequencing tech-nology. The size of the genome is reported as 16,767bp and comprises 13 protein-coding genes, 2rRNAs and 22 tRNAs. The organization of the genome is comparable to that of other bird species.A phylogenetic comparison mapped the relative relationship of Sarothrura ayresi with respect to otherspecies in the order Gruiformes.ARTICLE HISTORYReceived 15 March 2017Accepted 10 April 2017KEYWORDSWhite-winged flufftail; nextgeneration sequencing;critically endangeredThe Critically Endangered white-winged flufftail (Sarothruraayresi, WWFT) forms part of the genus Sarothrura (IUCN2015). The species is known from a limited number of highaltitude wetlands in South Africa with records fromNovember to March (austral summer), and more than4000km to the north, from only three sites in Ethiopia (fromJuly to September-boreal summer; Taylor 1994; De Smidt2003; Sande et al. 2008). It is estimated that there are only 50birds left in South Africa and perhaps only 250 throughout itsglobal range (BirdLife International 2015; Taylor et al. 2005).This small and enigmatic flufftail is threatened by the loss ofits wetland habitat (Davies et al. 2015). This critical endan-gered status of the WWFT is certainly the biggest drivingforce behind the ongoing research on this bird, particularly inorder to potentially develop conservation strategies thatcould enable the survival of the species. Sequence informa-tion on the family Sarothruridae of which the WWFT is amember, is scant in the current databases and as such isinadequate for the purpose of performing extensive genom-ics-based high throughput analyses to unravel information onphylogenetic relationships. Therefore, we determined thecomplete mitogenome sequence of the WWFT in order toserve as a resource for research.In the present study, a single specimen collected fromWakkerstroom, South Africa (2721’25.11"S, 3007’13.50"E) inJanuary 2014 was selected for mitochondrial analysis. Thiswas performed using standard extraction using the ZRGenomic DNATM – Tissue MiniPrep Kit (Zymo ResearchCorporation), library preparation and Illumina high-through-put sequencing (Illumina Inc., San Diego, CA). Sequenceswere assembled using the CLC Genomics platform (CLC Bio,Aarhus, Denmark). The mitogenome was assembled underthe de novo option, using the standard parameters. Variouskmer sizes were used during optimisation and the full mito-chondrial genome for the WWFT was assembled using kmersize 31. The mitochondrial assembly constituted 8597 readsout of the 18,567,330 that remained after quality trimmingand removal of contaminating adapters, using theTrimmomatic software (Bolger et al, 2014). Average genomecoverage of 53X was obtained for the assembly.The complete mitochondrial genome of the WWFT asdetermined in the study is 16,767 bp in length. The overallbase composition is 23.47% for A, 12.17% for C, 31.55 for Gand 32.78% for T. Prediction of protein-coding genes (PCGs)was performed using MITOS (Bernt et al. 2013), DOGMA(Wyman et al. 2004) as well as BLAST (Altschul et al. 1990)and curated through manual inspection. The gene content ofthe WWFT conforms to a typical vertebrate structure, consist-ing of 13 protein-coding genes (PCGs), 22 tRNAs and tworRNAs. The gene order of the WWFT also conforms to thestandard gene order in birds, using Gallus gallus as reference(Desjardins & Morais 1990). The 12 protein-coding genes, 2rRNAs and 14 tRNAs are encoded on the H strand and theremaining NAD6 and 8 tRNAs (trnE, trnP, trnS2, trnY, trnC,trnN, trnA and trnQ) are on the L strand. With the exceptionof COX1 (GTG), ND3 (ATC) and ND2 and ND5 (both ATA), therest of the PCGs use the standard ATG start codon. The ter-mination codons varied between TAA, TGA and TAG. The 22tRNAs range in size from 66 to 74 bp. The 12S rRNA is 965 bpin size whilst the 16S rRNA is 1605 bp. The mitochondrialgenome and its associated annotation were submitted tothe NCBI under Genbank accession number KY075897.CONTACT Desire L. Dalton desire@nzg.ac.za National Zoological Gardens of South Africa, Pretoria 0001, P.O. Box 754, South Africa 2017 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, dis-tribution, and reproduction in any medium, provided the original work is properly cited.MITOCHONDRIAL DNA PART B: RESOURCES, 2017VOL. 2, NO. 1, 236–237http://dx.doi.org/10.1080/23802359.2017.1318675The specimen and DNA obtained from the sample are cur-rently stored at the Biobank of the National ZoologicalGardens of South Africa.The WWFT mitogenome constitutes the first whole mito-chondrial genome entry within the Sarothruridae family. Inorder to evaluate its relative position within the orderGruiformes a phylogenetic tree (maximum-likelihood) wasconstructed to place the WWFT among species representingthe Rallidae, Gruidae, Heliornithidae and Otididae Familiesusing MEGA version 6 (Tamura et al. 2013). Whilst there aremore families classified within this order, these were individu-als from families that had whole mitochondrial genomesavailable. The Gallus gallus mitochondrial genome was usedas outgroup. The resultant phylogenetic tree, in Figure 1,indicates that the WWFT is closer associated with members ofthe Rallidae (Coturnicops exquisitis) and Heliornithidae(Heliornis fulica) than with members of the Gruidae(Anthropoides paradiseus) and Otidae (Otis tarda).Disclosure statementThe authors report no conflicts of interest. The authors alone are respon-sible for the content and writing of the paper.ReferencesAltschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic localalignment search tool. J Mol Biol. 215:403–410.Birdlife International. 2015. Global IUCN Red List for birds. [cited 2016July 15]. Available from: http://www.birdlife.org/datazone/species/fact-sheet/22692245Bernt M, Donath A, J€uhling F, Externbrink F, Florentz C, Fritzsch G, P€utz J,Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoanmitochondrial genome annotation. Mol Phylogenet Evol. 69:313–319.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer forIllumina Sequence Data. Bioinformatics. 30:2114–2120.Davies GBP, Smit-Robinson HA, Drummond IMM, Gardner B, Rautenbach S,Van Stuyvenberg D, Nattrass C, Pretorius M, Pietersen DW, Symes CT.2015. Recent records of the white-winged flufftail Sarothrura Ayresi(Aves, Sarothruridae) in South Africa, including details of a survey ofhigh-altitude wetlands in 2013–2014. Durban Nat Sci MuseumNovitates. 37:62–75.Desjardins P, Morais R. 1990. Sequence and gene organization of thechicken mitochondrial genome. A novel gene order in higher verte-brates. J Mol Biol. 212:599–634.De Smidt A. 2003. Ethiopian white-winged flufftail (Sarothrura ayresi)action plan. Johannesburg: BirdLife South Africa.IUCN. 2015. The IUCN Red List of Threatened Species. Version 2015-4.Sande E, Ndang’ang’a PK, Wakelin J, Wondafrash M, Drummond M,Dereliev S. (Compilers). 2008. International Single Species Action Planfor the Conservation of the White-winged Flufftail (Sarothrura ayresi).CMS Technical Series No. 19, AEWA Technical Series No. 38. Bonn,Germany.Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6:molecular evolutionary genetics analysis version 6.0. Mol Biol Evol.30:2725–2729.Taylor PB. 1994. The biology, ecology and conservation of four fluff tail spe-cies, Sarothrura (Aves: Rallidae). Pietermaritzburg: University of Natal.Taylor PB. 2005. White-winged Flufftail. In: Hockey PAR, Dean WRJ, RyanPG, editors. Roberts – birds of Southern Africa.Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organel-lar genomes with DOGMA. Bioinformatics. 20:3252–3255.Figure 1. Maximum-likelihood tree based on the GTR model of five species of birds within the order Gruiformes, with bootstrap percentages indicated. The tree wasrooted using Gallus gallus as outgroup.MITOCHONDRIAL DNA PART B: RESOURCES 237

Next generation sequencing yields the mitochondrial genome of the critically endangered Sarothrura ayresi (white-winged flufftail)

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Next generation sequencing yields the mitochondrial genome of the critically endangered Sarothrura ayresi (white-winged flufftail)

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