Advertisement

Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae)

Abstract

Based on only a handful of mitochondrial and nuclear loci, the phylogenetic relationships within the genus Acropora have been unclear. However, with the new sequencing technology of massively parallel sequencing (MPS), the inter-specific relationships within Acropora may be resolved. We performed multiplex sequencing of the mitochondrial genome of eleven Acropora species representing different groups using the Illumina Solexa platform. Mitochondrial genomes were sequenced from long PCR-amplified templates ligated with different index sequences (~9 kbp) and analyzed using the mitochondrial genome of Acropora tenuis as a reference. A total of 75 million read outputs in one Illumina lane were obtained, with mapping results having coverage up to 44,000-fold. Assembly results of multiplex samples confirmed with Sanger sequencing produced <0.03 % error. Aligning the eleven mitochondrial genomes with the reference sequence revealed only 110 phylogenetically informative sites over the mitochondrial genome. The largest pairwise genetic distance observed was in the putative control region (0.022). A comparison of two phylogenetic trees based on the whole mitochondrial genome and control region showed that the former tree produces a higher resolution of phylogenetic relationships. In this study, we demonstrated the first case of sequencing cnidarian mitochondrial genomes by using multiplex MPS and applying it in a phylogenomic analyses.

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Subscribe to journal

Immediate online access to all issues from 2019. Subscription will auto renew annually.

US$ 199

This is the net price. Taxes to be calculated in checkout.

Fig. 1
Fig. 2

References

  1. Ansorge W, Voss H, Zimmermann J (1997) DNA sequencing strategies. Wiley, New York

  2. Babcock R (1995) Synchronous multispecific spawning on coral reefs: potential for hybridization and roles of gamete recognition. Reprod Fert Develop 7:943–950

  3. Babcock RC, Bull GD, Harrison PL, Heyward AJ, Oliver JK, Wallace CC, Willis BL (1986) Synchronous spawnings of 105 scleractinian coral species on the Great Barrier Reef. Mar Biol 90:379–394

  4. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics: btu170

  5. Chen CA, Wallace CC, Wolstenholme J (2002) Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals. Mol Phylogenet Evol 23:137–149

  6. Chen IP, Tang CY, Chiou CY, Hsu JH, Wei NV, Wallace CC, Muir P, Wu H, Chen CA (2009) Comparative analyzes of coding and noncoding DNA regions indicate that Acropora (Anthozoa: Scleractina) possesses a similar evolutionary tempo of nuclear vs. mitochondrial genomes as in plants. Mar Biotechnol 11:141–152

  7. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e122

  8. Deng W, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, Sergei L, Pond K, Mullins JI (2010) DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques 48:405–408

  9. Doorduin L, Gravendee B, Lammers Y, Ariyurek Y, Woeng TCA, Vrieling K (2011) The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res 18:93–105

  10. Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1–15

  11. Faircloth BC, Sorenson L, Santini F, Alfaro ME (2013) A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS One 8:e65923

  12. Feldmeyer B, Hoffmeier K, Pfenninger M (2010) The complete mitochondrial genome of Radix balthica (Pulmonata, Basommatophora), obtained by low coverage shot gun next generation sequencing. Mol Phylogenet Evol 57:1329–1333

  13. Figueroa DF, Baco AR (2014) Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae. Deep-Sea Res Part II 99:83–91

  14. Fukami H, Omori M, Hatta M (2000) Phylogenetic relationships in the coral family Acroporidae, reassessed by inference from mitochondrial genes. Zool Sci 17:689–696

  15. Fukami H, Budd AF, Levitan DR, Jara J, Kersanach R, Knowlton N (2004) Geographic differences in species boundaries among members of the Montastraea Annularis complex based on molecular and morphological markers. Evolution 58:324–337

  16. Fukami H, Chen CA, Budd AF, Collins A, Wallace CC, Chuang YY, Chen C, Dai CF, Iwao K, Sheppard C, Knowlton N (2008) Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS One 3:e3222

  17. Harrison PL, Babcock RC, Bull GD, Oliver JK, Wallace CC, Willis BL (1984) Mass spawning in tropical reef corals. Science 223:1186–1189

  18. Hatta M, Fukami H, Wang W, Omori M, Shimoike K, Hayashibara T, Ina Y, Sugiyama T (1999) Reproductive and genetic evidence for a reticulate evolutionary history of mass-spawning corals. Mol Biol Evol 16:1607–1613

  19. Hellberg ME (2006) No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol Biol 6:24

  20. Huang D, Meier R, Todd PA, Chou LM (2008) Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol 66:167–174

  21. Huang D, Licuanan WY, Baird AH, Fukami H (2011) Cleaning up the “Bigmessidae”: molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evol Biol 11:37

  22. Hudson ME (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 8:3–17

  23. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754–755

  24. Jex AR, Hu M, Littlewood DTJ, Waeschenbach A, Gasser RB (2008) Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda). BMC Genomics 9:11

  25. Jex AR, Waeschenbach A, Hu M, van Wyk JA, Beveridge I, Littlewood DTJ, Gasser RB (2009a) The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum—two hookworms of animal health and zoonotic importance. BMC Genomics 10:79

  26. Jex AR, Hall RS, Littlewood DTJ, Gasser RB (2009b) An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res 382:522–533

  27. Kitahara MV, Cairns SD, Stolarski J, Blair D, Miller DJ (2010) A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS One 5:e11490

  28. Kitahara MV et al (2014) The “naked coral” hypothesis revisited—evidence for and against scleractinian monophyly. PLoS One 9:e94774

  29. Lin MF, Luzon KS, Licuanan WY, Ablan-Lagman MC, Chen CA (2011) Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa). Zool Stud 50:513–524

  30. Lin MF, Kitahara MV, Luo H, Tracey D, Geller J, Fukami H, Miller DJ, Chen CA (2014) Mitochondrial genome rearrangements in the scleractinia/corallimorpharia complex: implications for coral phylogeny. Genome Biol Evol 6:1086–1095

  31. McFadden CS, Benayahu E, Thoma JN, Nevarez PA, France SC (2011) Limitations of mitochondrial gene barcoding in Octocorallia. Mol Ecol Resour 11:19–31

  32. Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315–327

  33. Nakajima Y, Nishikawa A, Iguchi A, Sakai K (2012) The population genetic approach delineates the species boundary of reproductively isolated corymbose acroporid corals. Mol Phylogent Evol 63:527–531

  34. Odorico DM, Miller DJ (1997) Variation in the ribosomal internal transcribed spacers and 5.8 s rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution. Mol Biol Evol 14:465–473

  35. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818

  36. Richards Z, Miller DJ, Wallaces CC (2013) Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Mol Phylogenet Evol 69:837–851

  37. Romano SL, Palumbi SR (1996) Evolution of scleractinian corals inferred from molecular systematics. Science 271:640–642

  38. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

  39. Shearer TL, van Oppen MJH, Romano SL, Wörheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11:2475–2487

  40. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nature biotechnol 26:1135–1145

  41. Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, Bodeau J, Harris AN, Perry KM, Giaever G, Pourmand N, Nislow C (2010) Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38:e142

  42. Takahiro K (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 96:317–323

  43. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

  44. Timmermans M, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, Littlewood DT, Pons J, Vogler AP (2010) Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res 38:e197

  45. Tseng CC, Wallace CC, Chen CA (2005) Mitogenomic analysis of Montipora cactus and Anacropora matthai (Cnidaria; Scleractinia; Acroporidae) indicates an unequal rate of mitochondrial evolution among Acroporidae corals. Coral Reefs 24:502–508

  46. Tu J, Ge Q, Wang S, Wang L, Sun B, Yang Q, Bai Y, Lu Z (2012) Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis. BMC Genomics 13:43

  47. van Oppen MJH, Willis BL, Miller DJ (1999) Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora. Proc R Soc Lond B 266:179–183

  48. van Oppen MJH, Catmull J, McDonald BJ, Hislop NR, Hagerman PJ, Miller DJ (2000a) The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. J Mol Evol 55:1–13

  49. van Oppen MJH, Willis BL, Vugt HWJAV, Miller DJ (2000b) Examination of species boundaries in the Acropora cervicornis group (Scleractinia, Cnidaria) using nuclear DNA sequence analyzes. Mol Ecol 9:1363–1373

  50. van Oppen MJH, McDonald BJ, Willis BL, Miller DJ (2001) The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence? Mol Biol Evol 18:1315–1329

  51. van Oppen MJH, Willis BL, Van RT, Miller DJ (2002) Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in corals. Mol Ecol 11:1363–1376

  52. Veron JEN (2000) Corals of the world. Australian Institute of Marine Science, Townsville

  53. Veron JEN, Wallace CC (1984). Scleractinia of eastern Australia, Part V. Family Acroporidae AIMS Monogr Ser 6: 485

  54. Vollmer SV, Palumbi SR (2002) Hybridization and the evolution of coral reef diversity. Science 296:2023–2025

  55. Wallace CC (1999) Staghorn corals of the world: a revision of the genus Acropora. CSIRO Publishing, Collingwood

  56. Wallace CC, Willis BL (1994) Systematics of the coral genus Acropora: implications of new biological findings for species concepts. Annu Rev Ecol Syst 25:237–262

  57. Wallace CC, Wolstenholme J (1998) Revision of the coral genus Acropora (Scleractinia: Astrocoeniina: Acroporidae) in Indonesia. Zool J Linn Soc 123:199–384

  58. Wang M, Sun J, Li J, Qiu JW (2013) Complete mitochondrial genome of the brain coral Platygyra carnosus. Mitochondrial DNA 24:194–195

  59. Williams ST, Foster PG, Littlewood DTJ (2014) The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene 533:38–47

  60. Willis BL, Babcock RC, Harrison PL, Wallace CC (1997) Experimental hybridization and breeding incompatibilities within the mating systems of mass spawning reef corals. Coral Reefs 16:S53–S65

  61. Willis BL, van Oppen MJH, Miller DJ, Vollmer SV, Ayre DJ (2006) The role of hybridization in the evolution of reef corals. Ann Rev Ecol Evol Syst 37:489–517

  62. Wolstenholme JK (2004) Temporal reproductive isolation and gametic compatibility are evolutionary mechanisms in the Acropora humilis species group (Cnidaria; Scleractinia). Mar Biol 144:567–582

  63. Wolstenholme JK, Wallace CC, Chen CA (2003) Species boundaries within the Acropora humilis species group (Cnidaria; Scleractinia): a morphological and molecular interpretation of evolution. Coral Reefs 22:155–166

Download references

Acknowledgments

This project was funded by the National Science Council (2010–2012), Academia Sinica Thematic Grant (2006–2010), and the Biodiversity Research Centre, Academia Sinica (BRCAS) to CAC. We would like to thank the staffs of Penghu Marine Biological Research Centre (PMBRC)-BRCAS joint Marine Laboratory, BRCAS Green Island Reef Laboratory (GIRL) Green Island Marine Station, and Kenting National Park for assistance with fieldwork. Special thanks go to CREEG members and the David Miller Group for intellectual inputs to this paper, and to Tyler McCraney and Buford Pruitt, Jr. for English language editing. We also greatly thank three anonymous reviewers and the communicating editor for useful comments and suggestions to improve the manuscript.

Author information

Correspondence to Chaolun Allen Chen.

Additional information

Shang-Yin Vanson Liu and Chia-Ling Carynn Chan are co-first authors.

Communicated by C. Riginos.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 56 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Liu, S.V., Chan, C.C., Hsieh, H.J. et al. Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae). Mar Biol 162, 1383–1392 (2015) doi:10.1007/s00227-015-2657-1

Download citation

Keywords

  • Mitochondrial Genome
  • Sanger Sequencing
  • Sequence Assembly
  • Complete Mitochondrial Genome
  • Massively Parallel Sequencing