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