Reference
Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013). Predicting functional effect of human missense mutations using PolyPhen‐2.Current Protocols in Human Genetics , 76 (1), 7–20.
Ali, H., Haque, M. M., & Belton, B. (2013). Striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878) aquaculture in Bangladesh: an overview. Aquaculture Research , 44 (6), 950–965.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology , 215 (3), 403–410.
Atshaves, B. P., Martin, G. G., Hostetler, H. A., McIntosh, A. L., Kier, A. B., & Schroeder, F. (2010). Liver fatty acid-binding protein and obesity. The Journal of Nutritional Biochemistry , 21 (11), 1015–1032.
Bass, N. M. (1988). The cellular fatty acid binding proteins: aspects of structure, regulation, and function. In International review of cytology (Vol. 111, pp. 143–184). Elsevier.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2010). GenBank. Nucleic Acids Research ,39 (suppl_1), D32–D37.
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research , 27 (2), 573–580.
Birney, E., Clamp, M., & Durbin, R. (2004). GeneWise and genomewise.Genome Research , 14 (5), 988–995.
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., Estreicher, A., Gasteiger, E., … Phan, I. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research , 31 (1), 365–370.
Braissant, O., Foufelle, F., Scotto, C., Dauça, M., & Wahli, W. (1996). Differential expression of peroxisome proliferator-activated receptors (PPARs): tissue distribution of PPAR-alpha,-beta, and-gamma in the adult rat. Endocrinology , 137 (1), 354–366.
Campbell, M. S., Holt, C., Moore, B., & Yandell, M. (2014). Genome annotation and curation using MAKER and MAKER‐P. Current Protocols in Bioinformatics , 48 (1), 4–11.
Castresana, J. (2002). GBLOCKS: selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.Version 0.91 b. Copyrighted by J. Castresana, EMBL .
Chen, Y., Chen, Y., Shi, C., Huang, Z., Zhang, Y., Li, S., … Li, Z. (2018). SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience , 7 (1), gix120.
Choi, Y., & Chan, A. P. (2015). PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.Bioinformatics , 31 (16), 2745–2747.
Cifarelli, V., & Abumrad, N. A. (2011). Intestinal CD36 and other key proteins of lipid utilization: role in absorption and gut homeostasis.Comprehensive Physiology , 8 (2), 493–507.
Consortium, G. O. (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research ,32 (suppl_1), D258–D261.
De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006). CAFE: a computational tool for the study of gene family evolution.Bioinformatics , 22 (10), 1269–1271.
De Silva, S. S., Nguyen, T. T. T., Abery, N. W., & Amarasinghe, U. S. (2006). An evaluation of the role and impacts of alien finfish in Asian inland aquaculture. Aquaculture Research , 37 (1), 1–17.
De Silva, S. S., & Soto, D. (2009). Climate change and aquaculture: potential impacts, adaptation and mitigation. Climate Change Implications for Fisheries and Aquaculture: Overview of Current Scientific Knowledge. FAO Fisheries and Aquaculture Technical Paper ,530 , 151–212.
Desvergne, B., & Wahli, W. (1999). Peroxisome proliferator-activated receptors: nuclear control of metabolism. Endocrine Reviews ,20 (5), 649–688.
Dudchenko, O., Batra, S. S., Omer, A. D., Nyquist, S. K., Hoeger, M., Durand, N. C., … Aiden, A. P. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.Science , 356 (6333), 92–95.
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016). Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems , 3 (1), 95–98.
Flicek, P., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., … Fitzgerald, S. (2013). Ensembl. Nucleic Acids Res ,41 (2013), D48-55.
Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y., & Postlethwait, J. (1999). Preservation of duplicate genes by complementary, degenerative mutations. Genetics , 151 (4), 1531–1545.
Fornes, O., Castro-Mondragon, J. A., Khan, A., Van der Lee, R., Zhang, X., Richmond, P. A., … Baranašić, D. (2020). JASPAR 2020: update of the open-access database of transcription factor binding profiles.Nucleic Acids Research , 48 (D1), D87–D92.
Furuhashi, M., & Hotamisligil, G. S. (2008). Fatty acid-binding proteins: role in metabolic diseases and potential as drug targets.Nature Reviews Drug Discovery , 7 (6), 489–503.
Georgiadi, A., & Kersten, S. (2012). Mechanisms of gene regulation by fatty acids. Advances in Nutrition , 3 (2), 127–134.
Gertz, E. M., Yu, Y.-K., Agarwala, R., Schäffer, A. A., & Altschul, S. F. (2006). Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biology ,4 (1), 1–14.
Ghosh, S., & Chan, C.-K. K. (2016). Analysis of RNA-Seq data using TopHat and Cufflinks. In Plant Bioinformatics (pp. 339–361). Springer.
Guindon, S., Dufayard, J. F., Hordijk, W., Lefort, V., & Gascuel, O. (2009). PhyML: fast and accurate phylogeny reconstruction by maximum likelihood. Infection Genetics and Evolution , 9 (3), 384–385. ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS.
Hemung, B., Visetsunthorn, A., & Pariwat, S. (2010). Chemical properties and fatty acid profile of lipids extracted from freshwater fish species. Food Innovation Asia Conference 2010 Poster Presentation Proceedings , 669–675.
Hsu, M.-H., Palmer, C. N. A., Song, W., Griffin, K. J., & Johnson, E. F. (1998). A carboxyl-terminal extension of the zinc finger domain contributes to the specificity and polarity of peroxisome proliferator-activated receptor DNA binding. Journal of Biological Chemistry , 273 (43), 27988–27997.
Hsu, M. H. (n.d.). Novel Sequence Determinants in Peroxisome Proliferator Signaling. Journal of Biological Chemistry ,270 (27).
Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., … Duquenne, L. (2009). InterPro: the integrative protein signature database. Nucleic Acids Research ,37 (suppl_1), D211–D215.
Islami, S. N.-E., Reza, M. S., Mansur, M. A., Hossain, M. I., Shikha, F. H., & Kamal, M. (2014). Rigor index, fillet yield and proximate composition of cultured striped catfish (Pangasianodon hypophthalmus) for its suitability in processing industries in Bangladesh.Journal of Fisheries , 2 (3), 157–162.
Juge-Aubry, C., Pernin, A., Favez, T., Burger, A. G., Wahli, W., Meier, C. A., & Desvergne, B. (1997). DNA Binding Properties of Peroxisome Proliferator-activated Receptor Subtypes on Various Natural Peroxisome Proliferator Response Elements IMPORTANCE OF THE 5′-FLANKING REGION.Journal of Biological Chemistry , 272 (40), 25252–25259.
Jurka, J., Kapitonov, V. V, Pavlicek, A., Klonowski, P., Kohany, O., & Walichiewicz, J. (2005). Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research ,110 (1–4), 462–467.
Kanehisa, M., & Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research , 28 (1), 27–30.
Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature Methods ,12 (4), 357–360.
Kim, O. T. P., Nguyen, P. T., Shoguchi, E., Hisata, K., Vo, T. T. B., Inoue, J., … Kanda, M. (2018). A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement.BMC Genomics , 19 (1), 733.
Langdon, W. B. (2015). Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks.BioData Mining , 8 (1), 1.
Laprairie, R. B., Denovan-Wright, E. M., & Wright, J. M. (2016). Divergent evolution of cis-acting peroxisome proliferator-activated receptor elements that differentially control the tandemly duplicated fatty acid-binding protein genes, fabp1b. 1 and fabp1b. 2, in zebrafish.Genome , 59 (6), 403–412.
Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences.Bioinformatics , 34 (18), 3094–3100.
Li, L., Stoeckert, C. J., & Roos, D. S. (2003). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research , 13 (9), 2178–2189.
Lynch, M., & Conery, J. S. (2000). The evolutionary fate and consequences of duplicate genes. Science , 290 (5494), 1151–1155.
Pi, H., Liu, M., Xi, Y., Chen, M., Tian, L., Xie, J., … Yu, Z. (2019). Long‐term exercise prevents hepatic steatosis: a novel role of FABP1 in regulation of autophagy‐lysosomal machinery. The FASEB Journal , 33 (11), 11870–11883.
Pryszcz, L. P., & Gabaldón, T. (2016). Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Research ,44 (12), e113–e113.
Salmela, L., & Rivals, E. (2014). LoRDEC: accurate and efficient long read error correction. Bioinformatics , 30 (24), 3506–3514.
Shimizu, M., Takeshita, A., Tsukamoto, T., Gonzalez, F. J., & Osumi, T. (2004). Tissue-selective, bidirectional regulation of PEX11α and perilipin genes through a common peroxisome proliferator response element. Molecular and Cellular Biology , 24 (3), 1313–1323.
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V, & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics ,31 (19), 3210–3212.
Singh, A. K., & Lakra, W. S. (2012). Culture of Pangasianodon hypophthalmus into India: impacts and present scenario. Pakistan Journal of Biological Sciences , 15 (1), 19.
Smit, A. F. A., Hubley, R., & Green, P. (2014). RepeatModeler Open-1.0. 2008–2010. Access Date Dec .
Storch, J., & Thumser, A. E. A. (2000). The fatty acid transport function of fatty acid-binding proteins. Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids , 1486 (1), 28–44.
Tarailo‐Graovac, M., & Chen, N. (2009). Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics , 25 (1), 4–10.
Taylor, J. S., & Raes, J. (2004). Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. ,38 , 615–643.
Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2003). Multiple sequence alignment using ClustalW and ClustalX. Current Protocols in Bioinformatics , (1), 2–3.
Thompson, J., Winter, N., Terwey, D., Bratt, J., & Banaszak, L. (1997). The Crystal Structure of the Liver Fatty Acid-binding Protein A COMPLEX WITH TWO BOUND OLEATES. Journal of Biological Chemistry ,272 (11), 7140–7150.
Van Sang, N., Klemetsdal, G., Ødegård, J., & Gjøen, H. M. (2012). Genetic parameters of economically important traits recorded at a given age in striped catfish (Pangasianodon hypophthalmus).Aquaculture , 344 , 82–89.
Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017). Fast and accurate de novo genome assembly from long uncorrected reads.Genome Research , 27 (5), 737–746.
Venkatachalam, A. B., Parmar, M. B., & Wright, J. M. (2017). Evolution of the duplicated intracellular lipid-binding protein genes of teleost fishes. Molecular Genetics and Genomics , 292 (4), 699–727.
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., … Young, S. K. (2014). Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS One , 9 (11), e112963.
Wang, G., Bonkovsky, H. L., de Lemos, A., & Burczynski, F. J. (2015). Recent insights into the biological functions of liver fatty acid binding protein 1. Journal of Lipid Research , 56 (12), 2238–2247.
Xu, Z., & Wang, H. (2007). LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research , 35 (suppl_2), W265–W268.
Yang, Z. (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences ,13 (5), 555–556.
You, X., Shan, X., & Shi, Q. (2020). Research advances in the genomics and applications for molecular breeding of aquaculture animals.Aquaculture , 735357.
[dataset] Jieming Chen; Year: 2020; Pangasianodon hypophthalmus genome;CNGBdb (https://db.cngb.org/); ID: CNA0013719