Random PCR-based genotyping by sequencing technology GRAS-Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes.
SNP
direct
fish
genetic structure
genotyping by random amplicon sequencing
mangrove
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Sep 2019
Sep 2019
Historique:
received:
24
01
2019
revised:
06
04
2019
accepted:
15
04
2019
pubmed:
23
4
2019
medline:
18
1
2020
entrez:
23
4
2019
Statut:
ppublish
Résumé
While various technologies for high-throughput genotyping have been developed for ecological studies, simple methods tolerant to low-quality DNA samples are still limited. In this study, we tested the availability of a random PCR-based genotyping-by-sequencing technology, genotyping by random amplicon sequencing, direct (GRAS-Di). We focused on population genetic analysis of estuarine mangrove fishes, including two resident species, the Amboina cardinalfish (Fibramia amboinensis, Bleeker, 1853) and the Duncker's river garfish (Zenarchopterus dunckeri, Mohr, 1926), and a marine migrant, the blacktail snapper (Lutjanus fulvus, Forster, 1801). Collections were from the Ryukyu Islands, southern Japan. PCR amplicons derived from ~130 individuals were pooled and sequenced in a single lane on a HiSeq2500 platform, and an average of three million reads was obtained per individual. Consensus contigs were assembled for each species and used for genotyping of single nucleotide polymorphisms by mapping trimmed reads onto the contigs. After quality filtering steps, 4,000-9,000 putative single nucleotide polymorphisms were detected for each species. Although DNA fragmentation can diminish genotyping performance when analysed on next-generation sequencing technology, the effect was small. Genetic differentiation and a clear pattern of isolation-by-distance was observed in F. amboinensis and Z. dunckeri by means of principal component analysis, F
Identifiants
pubmed: 31009151
doi: 10.1111/1755-0998.13025
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1153-1163Subventions
Organisme : Japan Society for the Promotion of Science
ID : Grant-in-Aid for Scientific Research (A) 26252027
Informations de copyright
© 2019 John Wiley & Sons Ltd.
Références
Aburto-Oropeza, O., Dominguez-Guerrero, I., Cota-Nieto, J., & Plomozo-Lugo, T. (2009). Recruitment and ontogenetic habitat shifts of the yellow snapper (Lutjanus argentiventris) in the Gulf of California. Marine Biology, 156(12), 2461-2472. https://doi.org/10.1007/s00227-009-1271-5
Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655-1664. https://doi.org/10.1101/gr.094052.109
Allendorf, F. W., Hohenlohe, P. A., & Luikart, G. (2010). Genomics and the future of conservation genetics. Nature Reviews Genetics, 11(10), 697-709. https://doi.org/10.1038/nrg2844
Anderson, W. D. Jr, & Allen, G. R. (2001). Lutjanidae. Jobfishes. In K. E. Carpenter, & V. Niem (Eds.), FAO species identification guide for fishery purposes. The living marine resources of the Western Central Pacific. Vol. 5. Bony fishes part 3 (Menidae to Pomacentridae). (pp. 2840-2918). Rome, Italy: FAO.
Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe, P. A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17(2), 81-92. https://doi.org/10.1038/nrg.2015.28
Attard, C. R., Beheregaray, L. B., Sandoval-Castillo, J., Jenner, K. C. S., Gill, P. C., Jenner, M. N. M., … Möller, L. M. (2018). From conservation genetics to conservation genomics: A genome-wide assessment of blue whales (Balaenoptera musculus) in Australian feeding aggregations. Royal Society Open Science, 5(1), 170925.
Beck, M. W., Heck, K. L., Able, K. W., Childers, D. L., Eggleston, D. B., Gillanders, B. M., … Weinstein, M. P. (2001). The identification, conservation, and management of estuarine and marine nurseries for fish and invertebrates: A better understanding of the habitats that serve as nurseries for marine species and the factors that create site-specific variability in nursery quality will improve conservation and management of these areas. BioScience, 51(8), 633-641. https://doi.org/10.1641/0006-3568(2001)051[0633:TICAMO]2.0.CO;2
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
Bryan-Brown, D. N., Brown, C. J., Hughes, J. M., & Connolly, R. M. (2017). Patterns and trends in marine population connectivity research. Marine Ecology Progress Series, 585, 243-256. https://doi.org/10.3354/meps12418
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10(1), 421. https://doi.org/10.1186/1471-2105-10-421
Carreras, C., Ordóñez, V., Zane, L., Kruschel, C., Nasto, I., Macpherson, E., & Pascual, M. (2017). Population genomics of an endemic Mediterranean fish: Differentiation by fine scale dispersal and adaptation. Scientific Reports, 7, 43417. https://doi.org/10.1038/srep43417
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: Rising to the challenge of larger and richer datasets. Gigascience, 4(1), 7. https://doi.org/10.1186/s13742-015-0047-8
Cimino, M., Colin, P., Schramek, T., Lindfield, S., Domeier, M., & Terrill, E. (2018). Oceanographic, acoustic, and remote approaches reveal the spatio-temporal dynamics of blackfin snapper at an aggregation site in Palau. Marine Ecology Progress Series, 601, 185-201. https://doi.org/10.3354/meps12651
Collette, B. B., & Su, J. (1986). The halfbeaks (Pisces, Beloniformes, Hemiramphidae) of the Far East. Proceedings of the Academy of Natural Sciences of Philadelphia, 138(1), 250-301.
Cornuet, J. M., & Luikart, G. (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144(4), 2001-2014.
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A.,. … 1000 Genomes Project Analysis Group (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. https://doi.org/10.1093/bioinformatics/btr330
DiBattista, J. D., Travers, M. J., Moore, G. I., Evans, R. D., Newman, S. J., Feng, M., … Berry, O. (2017). Seascape genomics reveals fine-scale patterns of dispersal for a reef fish along the ecologically divergent coast of Northwestern Australia. Molecular Ecology, 26(22), 6206-6223. https://doi.org/10.1111/mec.14352
Enoki, H. (2019). The construction of psedomolecules of a commercial strawberry by DeNovoMAGIC and new genotyping technology, GRAS-Di. Proceedings of the Plant and Animal genome conference XXVII. San Diego, CA. Retrieved from https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/37002
Enoki, H., & Takeuchi, Y. (2018). New genotyping technology, GRAS-Di, using next generation sequencer. Proceedings of the Plant and Animal genome conference XXVI. San Diego, CA. Retrieved from https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29067
Etter, P. D., Bassham, S., Hohenlohe, P. A., Johnson, E. A., & Cresko, W. A. (2011). SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods in Molecular Biology, 772, 157-178.
Fox, J., & Weisberg, S. (2011). An R companion to applied regression, 2nd ed. Thousand Oaks, CA: Sage.
Gaither, M. R., Toonen, R. J., Robertson, D. R., Planes, S., & Bowen, B. W. (2010). Genetic evaluation of marine biogeographical barriers: Perspectives from two widespread Indo-Pacific snappers (Lutjanus kasmira and Lutjanus fulvus). Journal of Biogeography, 37(1), 133-147. https://doi.org/10.1111/j.1365-2699.2009.02188.x
Goudet, J. (2005). Hierfstat, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes, 5(1), 184-186. https://doi.org/10.1111/j.1471-8286.2004.00828.x
Hohenlohe, P. A., Amish, S. J., Catchen, J. M., Allendorf, F. W., & Luikart, G. (2011). Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11, 117-122. https://doi.org/10.1111/j.1755-0998.2010.02967.x
Inoue, H., Nanjo, K., Mizutani, A., Kitano, T., & Kohno, H. (2016). Spatiotemporal changes in fish assemblage structures in the Udara River, Amitori Bay, Iriomote Island. Japanese Journal of Ichthyology, 63(2), 63-79.
Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., … Itoh, T. (2014). Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Research, 24(8), 1384-1395. https://doi.org/10.1101/gr.170720.113
Kanai, T., Nanjo, K., Yamane, K., Amano, Y., Kohno, H., Watanabe, Y., & Sano, M. (2014). Utilization patterns of estuarine and marine habitats by the halfbeak Zenarchopterus dunckeri at Iriomote Island, southern Japan, evaluated from otolith microchemistry. Fisheries Science, 80(6), 1231-1239. https://doi.org/10.1007/s12562-014-0797-8
Keenan, K., McGinnity, P., Cross, T. F., Crozier, W. W., & Prodöhl, P. A. (2013). diveRsity: An R package for the estimation of population genetics parameters and their associated errors. Methods in Ecology and Evolution, 4(8), 782-788.
Kimura, M. (2000). Paleogeography of the Ryukyu Islands. Tropics, 10(1), 5-24.
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25(14), 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup (2009). The sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25(16), 2078-2079.
Lu, L. F., Miyazawa, Y., Cui, W., & Nadaoka, K. (2010). Numerical study of surface water circulation around Sekisei Lagoon, southwest Japan. Ocean Dynamics, 60(2), 359-375. https://doi.org/10.1007/s10236-010-0270-x
Masuda, H., Amaoka, K., Araga, C., Uyeno, T., & Yoshino, T. (1984). The fishes of the Japanese Archipelago. Tokyo, Japan: Tokai University Press.
Meirmans, P. G., & van Tienderen, P. H. (2004). Genotype and Genodive: Two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794. https://doi.org/10.1111/j.1471-8286.2004.00770.x
Nagelkerken, I., Blaber, S., Bouillon, S., Green, P., Haywood, M., Kirton, L. G., … Somerfield, P. J. (2008). The habitat function of mangroves for terrestrial and marine fauna: A review. Aquatic Botany, 89, 155-185. https://doi.org/10.1016/j.aquabot.2007.12.007
Nakabo, T. (2013). Fishes of Japan with pictorial keys to the species, 3rd ed. Hadano, Japan: Tokai University Press.
Nakamura, Y., Horinouchi, M., Shibuno, T., Tanaka, Y., Miyajima, T., Koike, I., … Sano, M. (2008). Evidence of ontogenetic migration from mangroves to coral reefs by black-tail snapper Lutjanus fulvus: Stable isotope approach. Marine Ecology Progress Series, 355, 257-266. https://doi.org/10.3354/meps07234
Nanjo, K., Kohno, H., Nakamura, Y., Horinouchi, M., & Sano, M. (2014). Differences in fish assemblage structure between vegetated and unvegetated microhabitats in relation to food abundance patterns in a mangrove creek. Fisheries Science, 80(1), 21-41.
Narum, S. R., Buerkle, C. A., Davey, J. W., Miller, M. R., & Hohenlohe, P. A. (2013). Genotyping-by-sequencing in ecological and conservation genomics. Molecular Ecology, 22(11), 2841-2847. https://doi.org/10.1111/mec.12350
Nelson, J. S., Grande, T. C., & Wilson, M. V. H. (2016). Fishes of the world, 5th ed. Hoboken, NJ: John Wiley & Sons.
Pantallano, A. D. S., Bobiles, R. U., & Nakamura, Y. (2018). Dependence of fish on subtropical riverine mangroves as habitat in the Ryukyu Islands, Japan. Fisheries Science, 84(4), 613-625. https://doi.org/10.1007/s12562-018-1202-9
Paradis, E., Claude, J., & Strimmer, K. (2004). APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290. https://doi.org/10.1093/bioinformatics/btg412
Paris, J. R., Sherman, K. D., Bell, E., Boulenger, C., Delord, C., El-Mahdi, M. B., … Stevens, J. R. (2018). Understanding and managing fish populations: Keeping the toolbox fit for purpose. Journal of Fish Biology, 92(3), 727-751.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81(3), 559-575. https://doi.org/10.1086/519795
Romañach, S. S., DeAngelis, D. L., Koh, H. L., Li, Y., Teh, S. Y., Barizan, R. S. R., & Zhai, L. (2018). Conservation and restoration of mangroves: Global status, perspectives, and prognosis. Ocean and Coastal Management, 154, 72-82. https://doi.org/10.1016/j.ocecoaman.2018.01.009
Rosewich, U. L., Pettway, R. E., McDonald, B. A., & Kistler, H. C. (1999). High levels of gene flow and heterozygote excess characterize Rhizoctonia solani AG-1 IA (Thanatephorus cucumeris) from Texas. Fungal Genetics and Biology, 28(3), 148-159. https://doi.org/10.1006/fgbi.1999.1174
Rudman, S. M., Barbour, M. A., Csilléry, K., Gienapp, P., Guillaume, F., Hairston Jr, N. G., … Levine, J. M. (2018). What genomic data can reveal about eco-evolutionary dynamics. Nature Ecology & Evolution, 2(1), 9. https://doi.org/10.1038/s41559-017-0385-2
Shibuno, T., Nakamura, Y., Horinouchi, M., & Sano, M. (2008). Habitat use patterns of fishes across the mangrove-seagrass-coral reef seascape at Ishigaki Island, southern Japan. Ichthyological Research, 55(3), 218-237. https://doi.org/10.1007/s10228-007-0022-1
Shimose, T., & Nanami, A. (2014). Age, growth, and reproductive biology of blacktail snapper, Lutjanus fulvus, around the Yaeyama Islands, Okinawa, Japan. Ichthyological Research, 61(4), 322-331. https://doi.org/10.1007/s10228-014-0401-3
Shirai, K., Koyama, F., Murakami-Sugihara, N., Nanjo, K., Higuchi, T., Kohno, H., … Sano, M. (2018). Reconstruction of the salinity history associated with movements of mangrove fishes using otolith oxygen isotopic analysis. Marine Ecology Progress Series, 593, 127-139. https://doi.org/10.3354/meps12514
Suyama, Y., & Matsuki, Y. (2015). MIG-seq: An effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Scientific Reports, 5, 16963. https://doi.org/10.1038/srep16963
Toda, M., Shokita, S., & Nishida, M. (2003). Origin of flora and fauna of Ryûkyû Islands. In M. Nishida, N. Shikatani, & S. Shokita (Eds.), The flora and fauna of inland waters in the Ryukyu Islands (pp. 25-32). Tokyo, Japan: Tokai University Press.
Vendrami, D. L. J., Telesca, L., Weigand, H., Weiss, M., Fawcett, K., Lehman, K., … Hoffman, J. I. (2017). RAD sequencing resolves fine-scale population structure in a benthic invertebrate: Implications for understanding phenotypic plasticity. Royal Society Open Science, 4(2), 160548. https://doi.org/10.1098/rsos.160548
Watanabe, Y., Kawamata, I., Matsuki, Y., Suyama, Y., Uehara, K., & Ito, M. (2018). Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet. Heredity, 121, 594-604. https://doi.org/10.1038/s41437-018-0064-3
Wee, A. K. S., Mori, G. M., Lira, C. F., Núñez-Farfán, J., Takayama, K., Faulks, L., … Kajita, T. (2018). The integration and application of genomic information in mangrove conservation. Conservation Biology, 33(1), 206-209. https://doi.org/10.1111/cobi.13140
Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38(6), 1358-1370.
Weiss, M., Weigand, H., Weigand, A. M., & Leese, F. (2018). Genome-wide single-nucleotide polymorphism data reveal cryptic species within cryptic freshwater snail species-The case of the Ancylus fluviatilis species complex. Ecology and Evolution, 8(2), 1063-1072.
Wickel, J., Jamon, A., Pinault, M., Durville, P., & Chabanet, P. (2014). Species composition and structure of marine fish communities of Mayotte Island (south-western Indian Ocean). Cybium, 38(3), 179-203.
Wickham, H. (2016). ggplot2: Elegant graphics for data analysis. New York, NY: Springer.
Wilson, G. A., & Rannala, B. (2003). Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163(3), 1177-1191.
Zapata, F. A., & Herrón, P. A. (2002). Pelagic larval duration and geographic distribution of tropical eastern Pacific snappers (Pisces: Lutjanidae). Marine Ecology Progress Series, 230, 295-300. https://doi.org/10.3354/meps230295