Published May 10, 2022 | Version v1
Journal article Open

Garypus sanasai Lin, Huang & Chang 2022, sp. nov.

  • 1. Department of Science Education, National Taipei University of Education, No.134, Sec.2, Heping E. Rd., Da'an District, Taipei City 10671, Taiwan. *Correspondence: E-mail: chiahao0928@gmail.com (Chang). Tel.: +886-4-23590121#32453.

Description

Chang, Chia-Hao (2022): Garypus sanasai Lin, Huang & Chang 2022, sp. nov. Zoological Studies 61 (16): 1-11, DOI: 10.6620/ZS.2022.61-16, URL: http://dx.doi.org/10.5281/zenodo.12827626

Files

source.pdf

Files (2.0 MB)

Name Size Download all
md5:d237d206e2acdf0f8f984bdb2e57003d
2.0 MB Preview Download

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:D237D206FFACDF0FFF98FFDB2E57003D

References

  • Baralle FE, Giudice J. 2017. Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol 18:437- 451. doi:10.1038/nrm.2017.27.
  • Bellingham J, Tarttelin EE, Foster RG, Wells DJ. 2003. Structure and evolution of the Teleost extraretinal rod-like opsin (errlo) and ocular rod opsin (rho) genes: Is teleost rho a retrogene? J Exp Zool Part B 297B:1-10. doi:10.1002/jez.b.18.
  • Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvak Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C. 2018. Ten things you should know about transposable elements. Genome Biol 19:199. doi:10.1186/ s13059-018-1577-z.
  • Carelli FN, Hayakawa T, Go Y, Imai H, Warnefors M, Kaessmann H. 2016. The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res 26:301-314. doi:10.1101/ gr.198473.115.
  • Chang C-H, Catchen J, Moran RL, Rivera-Colon AG, Wang Y-C, Fuller RC. 2021. Sequence analysis and ontogenetic expression patterns of cone opsin genes in the bluefin killifish (Lucania goodei). J Hered 112:357-366. doi:10.1093/jhered/esab017.
  • Chang C-H, Wang Y-C, Shao YT, Liu S-H. 2020. Phylogenetic analysis and ontogenetic changes in the cone opsins of the western mosquitofish (Gambusia affinis). PLoS ONE 15:e0240313. doi:10.1371/journal.pone.0240313.
  • Chinen A, Hamaoka T, Yamada Y, Kawamura S. 2003. Gene duplication and spectral diversification of cone visual pigments of zebrafish. Genetics 163:663-675. doi:10.1093/ genetics/163.2.663.
  • Cortesi F, Musilova Z, Stieb SM, Hart NS, Siebeck UE, Malmstrom M, Torresen OK, Jentoft S, Cheney KL, Marshall NJ, Carleton KL, Salzburger W. 2015. Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes. Proc Natl Acad Sci U S A 112:1493-1498. doi:10.1073/pnas.1417803112.
  • Dulai KS, von Dornum M, Mollon JD, Hunt DM. 1999. The evolution of trichromatic color vision by opsin gene duplication in new world and old world primates. Genome Res 9:629-638.
  • Ehlman SM, Sandkam BA, Breden F, Sih A. 2015. Developmental plasticity in vision and behavior may help guppies overcome increased turbidity. J Comp Physiol A 201:1125-1135. doi:10.1007/s00359-015-1041-4.
  • Escobar-Camacho D, Ramos E, Martins C, Carleton KL. 2017. The opsin genes of amazonian cichlids. Mol Ecol 26:1343-1356. doi:10.1111/mec.13957.
  • Fujiyabu C, Sato K, Utari NML, Ohuchi H, Shichida Y, Yamashita T. 2019. Evolutionary history of teleost intron-containing and intron-less rhodopsin genes. Sci Rep 9:10653. doi:10.1038/ s41598-019-47028-4.
  • Grabski DF, Broseus L, Kumari B, Rekosh D, Hammarskjold ML, Ritchie W. 2020. Intron retention and its impact on gene expression and protein diversity: a review and a practical guide. Wiley Interdiscip Rev-RNA 12:e1631. doi:10.1002/wrna.1631.
  • Harada Y, Matsuo M, Kamei Y, Goto M, Fukamachi S. 2019. Evolutionary history of the medaka long-wavelength sensitive genes and effects of artificial regression by gene loss on behavioural photosensitivity. Sci Rep 9:2726. doi:10.1038/ s41598-019-39978-6.
  • Hofmann CM, Marshall NJ, Abdilleh K, Patel Z, Siebeck UE, Carleton KL. 2012. Opsin evolution in damselfish: convergence, reversal, and parallel evolution across tuning sites. J Mol Evol 75:79-91. doi:10.1007/s00239-012-9525-0.
  • Iniguez LP, Hernandez G. 2017. The evolutionary relationship between alternative splicing and gene duplication. Front Genet 8:14. doi:10.3389/fgene.2017.00014.
  • Johnson AM, Stanis S, Fuller RC. 2013. Diurnal lighting patterns and habitat alter opsin expression and colour preferences in a killifish. Proc Biol Sci 280:20130796. doi:10.1098/ rspb.2013.0796.
  • Kabza M, Ciomborowska J, Makalowska I. 2014. RetrogeneDB- A database of animal retrogenes. Mol Biol Evol 31:1646-1648. doi:10.1093/molbev/msu139.
  • Kaessmann H, Vinckenbosch N, Long M. 2009. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 10:19-31. doi:10.1038/nrg2487.
  • Kawamura S, Kasagi S, Kasai D, Tezuka A, Shoji A, Takahashi A, Imai H, Kawata M. 2016. Spectral sensitivity of guppy visual pigments reconstituted in vitro to resolve association of opsins with cone cell types. Vision Res 127:67-73. doi:10.1016/ j.visres.2016.06.013.
  • Knudsen S. 1999. Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics 15:356-361. doi:10.1093/ bioinformatics/15.5.356.
  • Kuzmin E, Taylor JS, Boone C. 2022. Retention of duplicated genes in evolution. Trends Genet 38:59-72. doi:10.1016/ j.tig.2021.06.016.
  • Laver CRJ, Taylor JS. 2011. RT-qPCR reveals opsin gene upregulation associated with age and sex in guppies (Poecilia reticulata) - a species with color-based sexual selection and 11 visual-opsin genes. BMC Evol Biol 11:81. doi:10.1186/1471-2148-11-81.
  • Li B, Carey M, Workman JL. 2007. The role of chromatin during transcription. Cell 128:707-719. doi:10.1016/j.cell.2007.01.015.
  • Lin J-J, Wang F-Y, Li W-H, Wang T-Y. 2017. The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation. Sci Rep 7:15568. doi:10.1038/ s41598-017-15868-7.
  • Musilova Z, Cortesi F, Matschiner M, Davies WIL, Patel JS, Stieb SM, de Busserolles F, Malmstrom M, Torresen OK, Brown CJ, Mountford JK, Hanel R, Stenkamp DL, Jakobsen KS, Carleton KL, Jentoft S, Marshall J, Salzburger W. 2019. Vision using multiple distinct rod opsins in deep-sea fishes. Science 364:588- 592. doi:10.1126/science.aav4632.
  • O'Quin KE, Smith D, Naseer Z, Schulte J, Engel SD, Loh YHE, Streelman JT, Boore JL, Carleton KL. 2011. Divergence in cis -regulatory sequences surrounding the opsin gene arrays of African cichlid fishes. BMC Evol Biol 11:120. doi:10.1186/1471- 2148-11-120.
  • Pantzartzi CN, Pergner J, Kozmik Z. 2018. The role of transposable elements in functional evolution of amphioxus genome: the case of opsin gene family. Sci Rep 8:2506. doi:10.1038/s41598-018- 20683-9.
  • Picaud S, Pattnaik B, Hicks D, Forster V, Fontaine V, Sahel J, Dreyfus H. 1998. GABAA and GABAC receptors in adult porcine cones: evidence from a photoreceptor-glia co-culture model. J Physiol 513:33-42. doi:10.1111/j.1469-7793.1998.033by.x.
  • Pizzarelli R, Griguoli M, Zacchi P, Petrini EM, Barberis A, Cattaneo A, Cherubini E. 2020. Tuning GABAergic inhibition: Gephyrin molecular organization and functions. Neuroscience 439:125- 136. doi:10.1016/j.neuroscience.2019.07.036.
  • Pohl M, Milvertz FC, Mayer A, Vences M. 2015. Multigene phylogeny of cyprinodontiform fishes suggests continental radiations and a rogue taxon position of Pantanodon. Vertebr Zool 65:37-44.
  • Rangannan V, Bansal M. 2009. Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition. Mol Bio Syst 5:1758-1769. doi:10.1039/B906535K.
  • Rao MB, Didiano D, Patton JG. 2017. Neurotransmitter-regulated regeneration in the zebrafish retina. Stem Cell Rep 8:831-842. doi:10.1016/j.stemcr.2017.02.007.
  • Rennison DJ, Owens GL, Allison WT, Taylor JS. 2011. Intra-retinal variation of opsin gene expression in the guppy (Poecilia reticulata). J Exp Biol 214:3248-3254. doi:10.1242/jeb.057836.
  • Sandkam B, Dalton B, Breden F, Carleton K. 2018. Reviewing guppy color vision: integrating the molecular and physiological variation in visual tuning of a classic system for sensory drive. Curr Zool 64:535-545. doi:10.1093/cz/zoy047.
  • Sassoe-Pognetto M, Fritschy J-M. 2000. Mini-review: gephyrin, a major postsynaptic protein of GABAergic synapses. Eur J Neurosci 12:2205-2210. doi:10.1046/j.1460-9568.2000.00106.x.
  • Shen C-H. 2019. Diagnostic Molecular Biology. Academic Press, San Diego, CA, USA.
  • Tam KJ, Watson CT, Massah S, Kolybaba AM, Breden F, Prefontaine GG, Beischlag TV. 2011. Regulatory function of conserved sequences upstream of the long-wave sensitive opsin genes in teleost fishes. Vision Res 51:2295-2303. doi:10.1016/ j.visres.2011.09.010.
  • Terai Y, Miyagi R, Aibara M, Mizoiri S, Imai H, Okitsu T, Wada A, Takahashi-Kariyazono S, Sato A, Tichy H, Mrosso HDJ, Mzighani SI, Okada N. 2017. Visual adaptation in Lake Victoria cichlid fishes: depth-related variation of color and scotopic opsins in species from sand/mud bottoms. BMC Evol Biol 17:200. doi:10.1186/s12862-017-1040-x.
  • Tine M, Kuhl H, Teske PR, Reinhardt R. 2021. Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes. Ecol Evol 11:6546-6557. doi:10.1002/ece3.7507.
  • Tsujimura T, Hosoya T, Kawamura S. 2010. A single enhancer regulating the differential expression of duplicated redsensitive opsin genes in zebrafish. PLoS Genetics 6:e1001245. doi:10.1371/journal.pgen.1001245.
  • Venkatesh S, Workman JL. 2015. Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol 16:178-189. doi:10.1038/nrm3941.
  • Vinckenbosch N, Dupanloup I, Kaessmann H. 2006. Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 103:3220-3225. doi:10.1073/pnas.0511307103.
  • Ward MN, Churcher AM, Dick KJ, Laver CRJ, Owens GL, Polack MD, Ward PR, Breden F, Taylor JS. 2008. The molecular basis of color vision in colorful fish: Four Long Wave-Sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites. BMC Evol Biol 8:210. doi:10.1186/1471-2148-8-210.
  • Watanabe M, Maemura K, Kanbara K, Tamayama T, Hayasaki H. 2002. GABA and GABA receptors in the central nervous system and other organs. Int Rev Cytol 213:1-47. doi:10.1016/s0074- 7696(02)13011-7.
  • Watson CT, Gray SM, Hoffmann M, Lubieniecki KP, Joy JB, Sandkam BA, Weigel D, Loew E, Dreyer C, Davidson WS, Breden F. 2011. Gene duplication and divergence of long wavelengthsensitive opsin genes in the guppy, Poecilia reticulata. J Mol Evol 72:40-222. doi:10.1007/s00239-010-9426-z.
  • Watson CT, Lubieniecki KP, Loew E, Davidson WS, Breden F. 2010. Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri. BMC Evol Biol 10:87. doi:10.1186/1471- 2148-10-87.
  • Yang X-L. 2004. Characterization of receptors for glutamate and GABA in retinal neurons. Prog Neurobiol 73:127-150. doi:10.1016/j.pneurobio.2004.04.002.
  • Yazulla S, Studholme KM. 2001. Neurochemical anatomy of the zebrafish retina as determined by immunocytochemistry. J Neurocytol 30:551-592. doi:10.1023/a:1016512617484.
  • Yella VR, Kumar A, Bansal M. 2018. Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy. Sci Rep 8:4520. doi:10.1038/s41598-018-22129-8.
  • Yokoyama S. 2000. Molecular evolution of vertebrate visual pigments. Prog Retin Eye Res 19:385-491. doi:10.1016/s1350- 9462(00)00002-1.
  • Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variaiton in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Mol Ecol Resour 19:1447-1460. doi:10.1111/1755-0998.13062.
  • Zhong Z, Yang L, Zhang YE, Xue Y, He S. 2016. Correlated expression of retrocopies andparental genes in zebrafish. Mol Genet Genomics 291:723-737. doi:10.1007/s00438-015-1140-5.