Acknowledgement
이 논문은 2021년도 정부(해양수산부)의 재원으로 해양수산과학기술진흥원 포스트게놈다부처유전체사업의 지원을 받아 수행된 연구임(No. 20180430).
References
- Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. 2020. Opportunities and challenges in long-read sequencing data analysis. Genome Biol 21: 1-16. https://doi.org/10.1186/s13059-019-1906-x
- Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, Bento P, Da Silva C, Labadie K, Alberti A, et al. 2014. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun 5: 1-10.
- Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, et al. 2014. The genomic substrate for adaptive radiation in African cichlid fish. Nature 513: 375-381. https://doi.org/10.1038/nature13726
- Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, PayzinDogru D, Lee TJ, Leigh ND, Kuo T-H, Davis FG, et al. 2017. A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors. Cell Rep 18: 762-776. https://doi.org/10.1016/j.celrep.2016.12.063
- Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18: 810-820. https://doi.org/10.1101/gr.7337908
- Byrne A, Beaudin AE, Olsen HE, Jain M, Cole C, Palmer T, DuBois RM, Forsberg EC, Akeson M, Vollmers C. 2017. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat Commun 8: 1-11. https://doi.org/10.1038/s41467-016-0009-6
- Chapman RW, Reading BJ, Sullivan CV. 2014. Ovary transcriptome profiling via artificial intelligence reveals a transcriptomic fingerprint predicting egg quality in striped bass, Morone saxatilis. PLoS One 9: e96818. https://doi.org/10.1371/journal.pone.0096818
- Cheng H, Concepcion GT, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18: 170-175. https://doi.org/10.1038/s41592-020-01056-5
- Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, et al. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13: 1050-1054. https://doi.org/10.1038/nmeth.4035
- Conte MA, Gammerdinger WJ, Bartie KL, Penman DJ, Kocher TD. 2017. A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics 18: 1-19. https://doi.org/10.1186/s12864-016-3406-7
- D'Agaro E. 2018. Artificial intelligence used in genome analysis studies. Eurobiotech J 2: 78-88. https://doi.org/10.2478/ebtj-2018-0012
- Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM. 2007. Creating a honey bee consensus gene set. Genome Biol 8: 1-8. https://doi.org/10.1186/gb-2007-8-s1-s1
- FAO. 2018. GLOBEFISH Highlights 4th issue 2018. A quarterly update on world seafood markets. FAO Globefish Research Programme.
- Fu S, Ma Y, Yao H, Xu Z, Chen S, Song J, Au KF. 2018. IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing. Bioinformatics 34: 2168-2176. https://doi.org/10.1093/bioinformatics/bty098
- Gene ontology consortium. 2015. Gene ontology consortium: going forward. Nucleic Acids Res 43: D1049-D1056. https://doi.org/10.1093/nar/gku1179
- Gonzalez-Garay ML. 2016. Introduction to isoform sequencing using pacific biosciences technology (Iso-Seq). Transcriptomics and gene regulation. Springer. pp 141-160.
- Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 9: 1-22.
- He AY, Ning LJ, Chen LQ, Chen YL, Xing Q, Li JM, Qiao F, Li DL, Zhang ML, Du ZY. 2015. Systemic adaptation of lipid metabolism in response to low-and high-fat diet in Nile tilapia (Oreochromis niloticus). Physiol Rep 3: e12485. https://doi.org/10.14814/phy2.12485
- Henschel R, Lieber M, Wu L-S, Nista PM, Haas BJ, LeDuc RD. 2012. Trinity RNA-Seq assembler performance optimization. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond. ACM. New York. pp 1-8.
- Huang X, Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Res 9: 868-877. https://doi.org/10.1101/gr.9.9.868
- Hu Y, Fang L, Chen X, Zhong JF, Li M, Wang K. 2021. LIQA: long-read isoform quantification and analysis. Genome Biol 22: 1-21. https://doi.org/10.1186/s13059-020-02207-9
- Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. 2008. NCBI BLAST: a better web interface. Nucleic Acids Res 36: W5-W9. https://doi.org/10.1093/nar/gkn201
- Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, et al. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30: 1236-1240. https://doi.org/10.1093/bioinformatics/btu031
- Juanchich A, Bardou P, Rue O, Gabillard J-C, Gaspin C, Bobe J, Guiguen Y. 2016. Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing. BMC Genomics 17: 1-12. https://doi.org/10.1186/s12864-015-2294-6
- Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, et al. 2007. KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-D484. https://doi.org/10.1093/nar/gkm882
- Kang S, Kim JH, Jo E, Lee SJ, Jung J, Kim BM, Lee JH, Oh TJ, Yum S, Rhee JS, et al. 2020. Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequencing and Hi-C analysis. Mol Ecol Resour 20: 520-530. https://doi.org/10.1111/1755-0998.13132
- Kim B-M, Kang S, Ahn D-H, Jung S-H, Rhee H, Yoo JS, Lee J-E, Lee S, Han Y-H, Ryu K-B, et al. 2018. The genome of common long-arm octopus Octopus minor. Gigascience 7: giy119.
- Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37: 540-546. https://doi.org/10.1038/s41587-019-0072-8
- Koren S, Phillippy AM. 2015. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 23: 110-120. https://doi.org/10.1016/j.mib.2014.11.014
- Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27: 722-736. https://doi.org/10.1101/gr.215087.116
- Korf I. 2004. Gene finding in novel genomes. BMC Bioinform 5: 1-9. https://doi.org/10.1186/1471-2105-5-1
- Kuo RI, Cheng Y, Zhang R, Brown JW, Smith J, Archibald AL, Burt DW. 2020. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics 21: 1-22. https://doi.org/10.1186/s12864-019-6419-1
- Liang P, Saqib HSA, Ni X, Shen Y. 2020. Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). BMC Genomics 21: 1-15. https://doi.org/10.1186/s12864-019-6419-1
- Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin AJN, et al. 2016. The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200-205. https://doi.org/10.1038/nature17164
- Liu Q, Mackey AJ, Roos DS, Pereira FCN. 2008. Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction. Bioinformatics 24: 597-605. https://doi.org/10.1093/bioinformatics/btn004
- Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, et al. 2016. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun 7: 1-13.
- Logsdon GA, Vollger MR, Eichler EE. 2020. Long-read human genome sequencing and its applications. Nat Rev Genet 21: 597-614. https://doi.org/10.1038/s41576-020-0236-x
- Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M. 2005. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res 33: 6494-6506. https://doi.org/10.1093/nar/gki937
- Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, et al. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1: 2047-217X-1-18.
- Majoros WH, Pertea M, Salzberg SL. 2004. TigrScan and Glimmer-HMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20: 2878-2879. https://doi.org/10.1093/bioinformatics/bth315
- Marancik D, Gao G, Paneru B, Ma H, Hernandez AG, Salem M, Yao J, Palti Y, Wiens GD. 2015. Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Front Genet 5: 453. https://doi.org/10.3389/fgene.2014.00453
- Mennigen JA, Panserat S, Larquier M, Plagnes-Juan E, Medale F, Seiliez I, Skiba-Cassy S. 2012. Postprandial regulation of hepatic microRNAs predicted to target the insulin pathway in rainbow trout. PLoS One 7: e38604. https://doi.org/10.1371/journal.pone.0038604
- Mennigen JA, Skiba-Cassy S, Panserat S. 2013. Ontogenetic expression of metabolic genes and microRNAs in rainbow trout alevins during the transition from the endogenous to the exogenous feeding period. J Exp Biol 216: 1597-1608. https://doi.org/10.1242/jeb.082248
- Mennigen JA, Zhang D. 2016. MicroTrout: A comprehensive, genome-wide miRNA target prediction framework for rainbow trout, Oncorhynchus mykiss. Comp Biochem Physiol -D: Genome Proteom 20: 19-26.
- Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327. https://doi.org/10.1016/j.ygeno.2010.03.001
- Mittag F, Buchel F, Saad M, Jahn A, Schulte C, Bochdanovits Z, Simon-Sanchez J, Nalls MA, Keller M, Hernandez DG, et al. 2012. Use of support vector machines for disease risk prediction in genome-wide association studies: Concerns and opportunities. Hum Mutat 33: 1708-1718. https://doi.org/10.1002/humu.22161
- Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, et al. 2000. A whole-genome assembly of Drosophila. Science 287: 2196-2204. https://doi.org/10.1126/science.287.5461.2196
- Narum SR, Campbell NR. 2015. Transcriptomic response to heat stress among ecologically divergent populations of redband trout. BMC Genomics 16: 1-12. https://doi.org/10.1186/1471-2164-16-1
- Nath S, Shaw DE, White MA. 2021. Improved contiguity of the threespine stickleback genome using long-read sequencing. G3-GENES GENOM GENET 11: jkab007.
- Nemudryi A, Valetdinova K, Medvedev S, Zakian S. 2014. TALEN and CRISPR/Cas genome editing systems: tools of discovery. Acta Naturae 6.
- Rautiainen M, Durai DA, Chen Y, Xin L, Low HM, Goke J, Marschall T, Schulz MH. 2020. AERON: Transcript quantification and gene-fusion detection using long reads. bioRxiv 921338.
- Reading BJ, Chapman RW, Schaff JE, Scholl EH, Opperman CH, Sullivan CV. 2012. An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish. BMC Res Notes 5: 1-12. https://doi.org/10.1186/1756-0500-5-1
- Reading BJ, Williams VN, Chapman RW, Williams TI, Sullivan CV. 2013. Dynamics of the striped bass (Morone saxatilis) ovary proteome reveal a complex network of the translasome. J Proteome Res 12: 1691-1699. https://doi.org/10.1021/pr3010293
- Salem M, Vallejo RL, Leeds TD, Palti Y, Liu S, Sabbagh A, Rexroad III CE, Yao J. 2012. RNA-Seq identifies SNP markers for growth traits in rainbow trout. PLoS One 7: e36264. https://doi.org/10.1371/journal.pone.0036264
- Schulz MH, Zerbino DR, Vingron M, Birney E. 2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092. https://doi.org/10.1093/bioinformatics/bts094
- Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117-1123. https://doi.org/10.1101/gr.089532.108
- Sookruksawong S, Sun F, Liu Z, Tassanakajon A. 2013. RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei. Dev Comp Immunol 41: 523-533. https://doi.org/10.1016/j.dci.2013.07.020
- Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34: W435-W439. https://doi.org/10.1093/nar/gkl200
- Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrom M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, et al. 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477: 207-210. https://doi.org/10.1038/nature10342
- Sullivan CV, Chapman RW, Reading BJ, Anderson PE. 2015. Transcriptomics of mRNA and egg quality in farmed fish: some recent developments and future directions. Gen Comp Endocrinol 221: 23-30. https://doi.org/10.1016/j.ygcen.2015.02.012
- Tardaguila M, De La Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, et al. 2018. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Res 28: 396-411. https://doi.org/10.1101/gr.222976.117
- Valenzuela-Miranda D, Boltana S, Cabrejos ME, Yanez JM, Gallardo-Escarate C. 2015. High-throughput transcriptome analysis of ISAV-infected Atlantic salmon Salmo salar unravels divergent immune responses associated to head-kidney, liver and gills tissues. Fish Shellfish Immunol 45: 367-377. https://doi.org/10.1016/j.fsi.2015.04.003
- Wei J, Zhang X, Yu Y, Huang H, Li F, Xiang J. 2014. Comparative transcriptomic characterization of the early development in Pacific white shrimp Litopenaeus vannamei. PLoS One 9: e106201. https://doi.org/10.1371/journal.pone.0106201
- Wyman D, Balderrama-Gutierrez G, Reese F, Jiang S, Rahmanian S, Forner S, Matheos D, Zeng W, Williams B, Trout D. 2020. A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification. bioRxiv 672931.
- Xu C, Evensen O, Munang'Andu HM. 2015a. De novo assembly and transcriptome analysis of Atlantic salmon macrophage/dendritic-like TO cells following type I IFN treatment and Salmonid alphavirus subtype-3 infection. BMC Genomics 16: 1-16. https://doi.org/10.1186/1471-2164-16-1
- Xu Z, Gan L, Li T, Xu C, Chen K, Wang X, Qin JG, Chen L, Li E. 2015b. Transcriptome profiling and molecular pathway analysis of genes in association with salinity adaptation in Nile tilapia Oreochromis niloticus. PLoS One 10: e0136506. https://doi.org/10.1371/journal.pone.0136506
- Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829. https://doi.org/10.1101/gr.074492.107
- Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490: 49-54. https://doi.org/10.1038/nature11413
- Zhao Y, Wang J, Thammaratsuntorn J, Wu J, Wei J, Wang Y, Xu J, Zhao J. 2015. Comparative transcriptome analysis of Nile tilapia (Oreochromis niloticus) in response to alkalinity stress. Genet Mol 14: 17916-17926. https://doi.org/10.4238/2015.December.22.16
- Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. 2013. The MaSuRCA genome assembler. Bioinformatics 29: 2669-2677. https://doi.org/10.1093/bioinformatics/btt476