Effect of high temperatures on sex ratio and differential expression analysis (RNA-seq) of sex-determining genes in <i>Oreochromis niloticus</i> from different river basins in Benin
Fagbemi, Mohammed Nambyl Adéoti; Nivelle, Renaud; Muller, Marcet al.
Health, Toxicology and Mutagenesis; Genetics (clinical); Genetics; Molecular Biology
Abstract :
[en] Abstract
The high temperature sex reversal process leading to functional phenotypic masculinization during development has been widely described in Nile tilapia (Oreochromis niloticus) under laboratory or aquaculture conditions and in the wild. In this study, we selected five wild populations of O. niloticus from different river basins in Benin and produced twenty full-sib families of mixed-sex (XY and XX) by natural reproduction. Progenies were exposed to room temperature or high (36.5°C) temperatures between 10 and 30 days post-fertilization (dpf). In control groups, we observed sex ratios from 40 to 60% males as expected, except for 3 families from the Gobé region which showed a bias towards males. High temperature treatment significantly increased male rates in each family up to 88%. Transcriptome analysis was performed by RNA-sequencing (RNA-seq) on brains and gonads from control and treated batches of six families at 15 dpf and 40 dpf. Analysis of differentially expressed genes, differentially spliced genes, and correlations with sex reversal was performed. In 40 dpf gonads, genes involved in sex determination such as dmrt1, cyp11c1, amh, cyp19a1b, ara, and dax1 were upregulated. In 15 dpf brains, a negative correlation was found between the expression of cyp19a1b and the reversal rate, while at 40 dpf a negative correlation was found between the expression of foxl2, cyp11c1, and sf1 and positive correlation was found between dmrt1 expression and reversal rate. Ontology analysis of the genes affected by high temperatures revealed that male sex differentiation processes, primary male sexual characteristics, autophagy, and cilium organization were affected. Based on these results, we conclude that sex reversal by high temperature treatment leads to similar modifications of the transcriptomes in the gonads and brains in offspring of different natural populations of Nile tilapia, which thus may activate a common cascade of reactions inducing sex reversal in progenies.
Research center :
FOCUS - Freshwater and OCeanic science Unit of reSearch - ULiège [BE] GIGA Platform Genomics
Disciplines :
Genetics & genetic processes
Author, co-author :
Fagbemi, Mohammed Nambyl Adéoti ; Université de Liège - ULiège > Freshwater and OCeanic science Unit of reSearch (FOCUS) ; Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi , 01 BP: 526 Cotonou, Benin
Nivelle, Renaud ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Gestion des ressources aquatiques et aquaculture
Muller, Marc ; Université de Liège - ULiège > GIGA > GIGA Cancer - Molecular Angiogenesis Laboratory
Mélard, Charles ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution
Lalèyè, Philippe; Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi , 01 BP: 526 Cotonou, Benin
Rougeot, Carole ; Université de Liège - ULiège > Freshwater and OCeanic science Unit of reSearch (FOCUS)
Language :
English
Title :
Effect of high temperatures on sex ratio and differential expression analysis (RNA-seq) of sex-determining genes in <i>Oreochromis niloticus</i> from different river basins in Benin
Cutting A, Chue J, Smith CA. Just how conserved is vertebrate sex determination?. Dev Dyn 2013;242:380–7.
Devlin RH, Nagahama Y. Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture 2002;208:191–364.
Hayes TB. Sex determination and primary sex differentiation in amphibians: genetic and developmental mechanisms. J Exp Zool 1998;281:373–99.
Fricke R, Eschmeyer WN, Van der Laan R (eds), Eschmeyer’s Catalog of Fishes: Genera, Species, References. Fishbase, 2020.
Sandra G-E, Norma -M-M. Sexual determination and differentiation in teleost fish. Rev Fish Biol Fish 2010;20:101–21.
Baroiller JF, D’Cotta H, Bezault E et al. Tilapia sex determination: where temperature and genetics meet. Comp Biochem Physiol - A Mol Integr Physiol 2009;153:30–8.
Cnaani A, Lee BY, Zilberman N et al. Genetics of sex determination in tilapiine species. Sex Dev 2008;2:43–54.
Lee BY, Penman DJ, Kocher TD. Identification of a sex-determining region in Nile tilapia (Oreochromis niloticus) using bulked segregant analysis. Anim Genet 2003;34: 379–83.
Shirak A, Seroussi E, Cnaani A et al. Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within quantitative trait locus regions for sex determination. Genetics 2006;174:1573–81.
Bezault E, Clota F, Derivaz M et al. Sex determination and temperature-induced sex differentiation in three natural populations of Nile tilapia (Oreochromis niloticus) adapted to extreme temperature conditions. Aquaculture 2007;272:S3–16.
Müller-Belecke A, Hörstgen-Schwark G. Sex determination in tilapia (Oreochromis niloticus) sex ratios in homozygous gynogenetic progeny and their offspring. Aquaculture 1995;137:57–65.
Baroiller J-F, Clota F, Geraz E. Temperature sex determination in two Tilapia, Oreochromis niloticus and the red Tilapia (red Florida strain): effect of high or low temperature. 1995.
Baroiller JF, Chourrout D, Fostier A et al. Temperature and sex chromosomes govern sex ratios of the mouthbrooding Cichlid fish Oreochromis niloticus. J Exp Zool 1995;273:216–23.
Wessels S, Hörstgen-Schwark G. Selection experiments to increase the proportion of males in Nile tilapia (Oreochromis niloticus) by means of temperature treatment. Aquaculture 2007;272:80–7.
Baroiller JF, D’Cotta H, Saillant E. Environmental effects on fish sex determination and differentiation. Sex Dev 2009;3:118–35.
Tessema M, Müller-Belecke A, Hörstgen-Schwark G. Effect of rearing temperature on the sex ratios of Oreochromis niloticus populations. Aquaculture 2006;258:270–7.
Saito D, Tanaka M. Comparative aspects of gonadal sex differentiation in medaka: a conserved role of developing oocytes in sexual canalization. Sex Dev 2009;3:99–107.
Berbejillo J, Martinez-Bengochea A, Bedo G et al. Expression and phylogeny of candidate genes for sex differentiation in a primitive fish species, the Siberian sturgeon. Acipenser baerii. Mol Reprod Dev 2012;79:504–16.
Penman DJ, Piferrer F. Fish gonadogenesis. Part I: genetic and environmental mechanisms of sex determination. Rev Fish Sci 2008;16:16–34.
Conover DO, Kynard BE. Environmental sex determination: interaction of temperature and genotype in a fish. Science 1981;213:577–9.
Ospina-Álvarez N, Piferrer F, Chave J. Temperature-dependent sex determination in fish revisited: prevalence, a single sex ratio response pattern, and possible effects of climate change. Chave J, editor. PLoS One 2008;3:e2837.
Santi S, Gennotte V, Muller M et al. Sex-ratio, early sex steroid profiles and cyp19a1b, dmrt1 and foxl2 gene expressions upon high temperature treatment of undi ff erentiated African cat fi sh juveniles (Clarias gariepinus). Aquaculture 2019;499: 140–8.
Valenzuela N, Neuwald JL, Literman R. Transcriptional evolution underlying vertebrate sexual development. Dev Dyn 2013;242:307–19.
Díaz N, Piferrer F. Lasting effects of early exposure to temperature on the gonadal transcriptome at the time of sex differentiation in the European sea bass, a fish with mixed genetic and environmental sex determination. BMC Genomics 2015;16:1–16.
Navarro-Martín L, Viñas J, Ribas L et al. DNA methylation of the gonadal aromatase (cyp19a) promoter is involved in temperature-dependent sex ratio shifts in the European sea bass. PLoS Genet 2011;7:e1002447.
Yamaguchi T, Yamaguchi S, Hirai T et al. Follicle-stimulating hormone signaling and Foxl2 are involved in transcriptional regulation of aromatase gene during gonadal sex differentiation in Japanese flounder, Paralichthys olivaceus. Biochem Biophys Res Commun 2007;359:935–40.
Fernandino JI, Hattori RS, Kimura H et al. Expression profile and estrogenic regulation of anti-müllerian hormone during gonadal development in pejerrey Odontesthes bonariensis, a teleost fish with strong temperature-dependent sex determination. Dev Dyn 2008;237:3192–9.
Dcotta H, Fostier A, Guiguen Y et al. Search for genes involved in the temperature-induced gonadal sex differentiation in the tilapia, Oreochromis niloticus. J Exp Zool 2001;290:574–85.
Poonlaphdecha S, Pepey E, Canonne M et al. Temperature induced-masculinisation in the Nile tilapia causes rapid upregulation of both dmrt1 and amh expressions. Gen Comp Endocrinol 2013;193:234–42.
D’Cotta H, Fostier A, Guiguen Y et al. Aromatase plays a key role during normal and temperature-induced sex differentiation of Tilapia Oreochromis niloticus. Mol Reprod Dev 2001;59:265–76.
Ijiri S, Kaneko H, Kobayashi T et al. Sexual dimorphic expression of genes in gonads during early differentiation of a teleost fish, the Nile Tilapia Oreochromis niloticus. Biol Reprod 2008;78:333–41.
Li CG, Wang H, Chen HJ et al. Differential expression analysis of genes involved in high-temperature induced sex differentiation in Nile tilapia. Comp Biochem Physiol Part - B Biochem Mol Biol 2014;177–178:36–45.
Lee KH, Yamaguchi A, Rashid H et al. Germ cell degeneration in high-temperature treated pufferfish, Takifugu rubripes. Sex Dev 2009;3:225–32.
Wu GC, Tomy S, Lee MF et al. Sex differentiation and sex change in the protandrous black porgy, Acanthopagrus schlegeli. Gen Comp Endocrinol 2010;167:417–21.
Nakamura S, Kurokawa H, Asakawa S et al. Two distinct types of theca cells in the medaka gonad: germ cell-dependent maintenance of cyp19a1-expressing theca cells. Dev Dyn 2009;238:2652–7.
Lin Q, Mei J, Li Z et al. Distinct and cooperative roles of amh and dmrt1 in self-renewal and differentiation of male germ cells in zebrafish. Genetics 2017;207:1007–22.
Webster KA, Schach U, Ordaz A et al. Dmrt1 is necessary for male sexual development in zebrafish. Dev Biol 2017;422:33–46.
Dai S, Qi S, Wei X et al. Germline sexual fate is determined by the antagonistic action of dmrt1 and foxl3/foxl2 in tilapia. Development 2021;148:dev199380.
Sissao R, D’Cotta H, Baroiller J-F et al. Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus . PeerJ 2019;7:e7709.
Fagbemi MNA, Oloukoule R, Lederoun D et al. Comparative study of the breeding performances of five populations of Nile tilapia (Oreochromis niloticus) (F1) in an experimental ongrowing system in Benin (West Africa). J Appl Aquac 2023;35:83–99.
Fagbémi MNA, Pigneur L-M, Adrien A et al. Genetic structure of wild and farmed Nile tilapia (Oreochromis niloticus) populations in Benin based on genome wide SNP technology. Aquaculture 2021;535:736432.
Baras E, Jacobs B, Mélard C. Effect of water temperature on survival, growth and phenotypic sex of mixed (XX-XY) progenies of Nile tilapia Oreochromis niloticus. Aquaculture 2001;192:187–99.
Baroiller JF, D’Cotta H. Environment and sex determination in farmed fish. Comp Biochem Physiol - C Toxicol Pharmacol 2001;130:399–409.
Ribas L, Liew WC, Díaz N et al. Heat-induced masculinization in domesticated zebrafish is family-specific & yields a set of different gonadal transcriptomes. Proc Natl Acad Sci U S A 2017;114:E941–50.
Azaza MS, Dhraïef MN, Kraïem MM. Effects of water temperature on growth and sex ratio of juvenile Nile tilapia Oreochromis niloticus (Linnaeus) reared in geothermal waters in southern Tunisia. J Therm Biol 2008;33:98–105.
Pandit NP, Nakamura M. Effect of high temperature on survival, growth and feed conversion ratio of Nile Tilapia, Oreochromis niloticus. Our Nat 2010;8:219–24.
Abucay JS, Mair GC, Skibinski DOF et al. Environmental sex determination: the effect of temperature and salinity on sex ratio in Oreochromis niloticus. L. Aquaculture 1999;173:219–34.
Karayücel I, Penman D, Karayücel S et al. Thermal and hormonal feminization of all male YY Nile tilapia, Oreochromis niloticus L. Isr J Aquac - Bamidgeh 2003;55:114–22.
Shao C, Li Q, Chen S et al. Epigenetic modification and inheritance in sexual reversal of fish. Genome Res 2014;24:604–15.
Wessels S, Samavati S, Hörstgen-Schwark G. Effect of early temperature treatments on sex differentiation in Nile tilapia, Oreochromis niloticus lines selected for high and low thermosensitivity. Aquaculture 2011;316:139–42.
Kim Y, Capel B. Balancing the bipotential gonad between alternative organ fates: a new perspective on an old problem. Dev Dyn an off Publ Am Assoc Anat 2006;235:2292–300.
Munger SC, Capel B. Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. Wiley Interdiscip Rev Syst Biol Med 2012;4:401–12.
Barrionuevo FJ, Burgos M, Scherer G et al. Genes promoting and disturbing testis development. Histol Histopathol 2012;27:1361–83.
Piferrer F. Epigenetics of sex determination and gonadogenesis. Dev Dyn 2013;242:360–70.
Filby AL, Tyler CR. Molecular characterization of estrogen receptors 1, 2a, and 2b and their tissue and ontogenic expression profiles in Fathead Minnow (Pimephales promelas)1. Biol Reprod 2005;73:648–62.
Matson CK, Zarkower D. Sex and the singular DM domain: insights into sexual regulation, evolution and plasticity. Nat Rev Genet 2012;13:163.
Vernetti CHMM, Mariacute Lia DNR, Gutierrez HJP et al. Genes involved in sex determination and the influence of temperature during the sexual differentiation process in fish: A review. African J Biotechnol 2012;12:2129–46.
Johnsen H, Tveiten H, Torgersen JS et al. Divergent and sex-dimorphic expression of the paralogs of the Sox9-Amh-Cyp19a1 regulatory cascade in developing and adult atlantic cod (Gadus morhua. L.). Mol Reprod Dev 2013;80:358–70.
Santi S, Gennotte V, Toguyeni A et al. Thermosensitivity of the sex differentiation process in the African catfish, Clarias gariepinus: determination of the thermosensitive period. Aquaculture 2016;455:73–80.
Jørgensen A, Morthorst JE, Andersen O et al. Expression profiles for six zebrafish genes during gonadal sex differentiation. Reprod Biol Endocrinol 2008;6:1–12.
Wang DS, Kobayashi T, Zhou LY et al. Molecular cloning and gene expression of Foxl2 in the Nile tilapia, Oreochromis niloticus. Biochem Biophys Res Commun 2004;320:83–9.
Gennotte V, Mélard C, d’Cotta H et al. The sensitive period for male-to-female sex reversal begins at the embryonic stage in the Nile tilapia and is associated with the sexual genotype. Mol Reprod Dev 2014;81:1146–58.
Rougeot C, Prignon C, Ngouana Kengne CV et al. Effect of high temperature during embryogenesis on the sex differentiation process in the Nile tilapia, Oreochromis niloticus. Aquaculture 2008;276:205–8.
Bromberg KD, Mitchell TRH, Upadhyay AK et al. The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity. Nat Chem Biol 2017;13:317–24.
Wu H, Siarheyeva A, Zeng H et al. Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2. FEBS Lett 2013;587:3859–68.
Piferrer F, Blázquez M, Viñas J et al. Temperature-dependent sex determination in fish. Effects of temperature on Gonadal Aromatase gene expression and epigenetic regulation after early exposure to high water temperature. 2008; http://hdl.handle.net/10261/80750 (11/23/2023).
Anastasiadi D. Intrinsic and environmental influences on DNA methylation and gene expression in fish. 2016. http://hdl.handle.net/10261/143896 (11/23/2023)
Lallias D, Quillet E, Dupont-Nivet M et al. AMETHYST: METHYlation analysis after temperature stress in trout. In: 3 Journée de Séminaires du Département Phase sur l’Epigénétique EpiPhase. 2017. p. np. https://hal.science/hal-01605305 (11/23/2023).
Lord CC, Thomas G, Brown JM. Mammalian alpha beta hydrolase domain (ABHD) proteins: lipid metabolizing enzymes at the interface of cell signaling and energy metabolism. Biochim Biophys Acta (BBA)-Molecular Cell Biol Lipids 2013;1831: 792–802.
Simpson CD, Hurren R, Kasimer D et al. A genome wide shRNA screen identifies α/β hydrolase domain containing 4 (ABHD4) as a novel regulator of anoikis resistance. Apoptosis 2012;17:666–78.
Strüssmann CA, Saito T, Takashima F. Heat-induced germ cell deficiency in the Teleosts Odontesthes bonariensis and Patagonina hatcheri. Comp Biochem Physiol Part A Mol Integr Physiol 1998;119:637–44.
Ito LS, Yamashita M, Strüssmann CA. Histological process and dynamics of germ cell degeneration in pejerrey Odontesthes bonariensis larvae and juveniles during exposure to warm water. J Exp Zool Part A Ecol Genet Physiol 2003;297:169–79.
Wang X, Liu Q, Xiao Y et al. High temperature causes masculinization of genetically female olive fl ounder (Paralichthys olivaceus) accompanied by primordial germ cell proliferation detention. Aquaculture 2017;479:808–16.
Chen S, Jiao L, Shubbar M et al. Unique structural platforms of Suz12 dictate distinct classes of PRC2 for chromatin binding. Mol Cell 2018;69:840–52.
Pasini D, Cloos PAC, Walfridsson J et al. JARID2 regulates binding of the polycomb repressive complex 2 to target genes in ES cells. Nature 2010;464:306–10.
Emili A, Greenblatt J, Wodak S. Systems Analysis of Chromatin-related Protein Complexes in Cancer. Springer & Business Media, 2013.
Guo L The molecular mechanisms of sex determination in vertebrates. Phd-Thesis, University of North Dakota, 2017:95–132.
Capel B. Vertebrate sex determination: evolutionary plasticity of a fundamental switch. Nat Rev Genet 2017;18:675.
Crespo D, Assis LHC, Van De Kant HJG et al. Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: follicle-stimulating hormone, retinoic acid and androgens. Development 2019;146.
Shen Y, Li Y, Zhu M et al. Transcriptional changes caused by estrogenic endocrine disrupting chemicals in gonad-mesonephros complexes of genetic male Xenopus laevis: multiple biomarkers for early detection of testis differentiation disruption. Sci Total Environ 2020;726:138522.
Du X, Wang B, Liu X et al. Comparative transcriptome analysis of ovary and testis reveals potential sex-related genes and pathways in spotted knifejaw Oplegnathus punctatus. Gene 2017;637:203–10.
Wang R, Wen L, Ma H et al. Effects of gonadotropin-releasing hormone analog (GnRHa) immunization on the gonadal transcriptome and proteome of tilapia (Oreochromis niloticus). Comp Biochem Physiol Part D 2021;37:100780.
Wainwright EN, Svingen T, Ng ET et al. Primary cilia function regulates the length of the embryonic trunk axis and urogenital field in mice. Dev Biol 2014;395.
Piprek RP, Damulewicz M, Tassan JP et al. Transcriptome profiling reveals male- and female-specific gene expression pattern and novel gene candidates for the control of sex determination and gonad development in Xenopus laevis. Dev Genes Evol 2019;229:53–72.
Altenhofen S, Nabinger DD, Pereira TCB et al. Manganese (II) chloride alters nucleotide and nucleoside catabolism in zebrafish (Danio rerio) adult brain. Mol Neurobiol. 2018;55:3866–74.
Böhne A, Sengstag T, Salzburger W. Comparative transcriptomics in East African cichlids reveals sex-and species-specific expression and new candidates for sex differentiation in fishes. Genome Biol Evol 2014;6:2567–85.
Tellez-Bañuelos MC, Ortiz-Lazareno PC, Santerre A et al. Effects of low concentration of endosulfan on proliferation, ERK1/2 pathway, apoptosis and senescence in Nile tilapia (Oreochromis niloticus) splenocytes. Fish Shellfish Immunol 2011;31:1291–6.
Zhao Y, Wang J, Thammaratsuntorn J et al. Comparative transcriptome analysis of Nile tilapia (Oreochromis niloticus) in response to alkalinity stress. Genet Mol Res 2015;14:17916–26.
Hong Xia J, Bai Z, Meng Z et al. Signatures of selection in tilapia revealed by whole genome resequencing. Sci Rep 2015;5:1–10.
Jung CH, Ro S-H, Cao J et al. mTOR regulation of autophagy. FEBS Lett 2010;584:1287–95.
Sengupta S, Peterson TR, Sabatini DM. Regulation of the mTOR complex 1 pathway by nutrients, growth factors, and stress. Mol Cell 2010;40:310–22.
Hu J, Zhang Z, Shen W-J et al. Cellular cholesterol delivery, intracellular processing and utilization for biosynthesis of steroid hormones. Nutr Metab (Lond) 2010;7:47.
Sun L-X, Wang -Y-Y, Zhao Y et al. Global DNA methylation changes in Nile tilapia gonads during high temperature-induced masculinization. PLoS One 2016;11:e0158483.
Y-h L, Wang H-P, Yao H et al. De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens. PLoS One 2017;12:e0171187.
Delaney MA, Klesius PH, Shelby RA. Cortisol response of Nile tilapia, Oreochromis niloticus (L.), to temperature changes. J Appl Aquac 2005;16:95–104.
Chadwick JG Jr, Nislow KH, McCormick SD. Thermal onset of cellular and endocrine stress responses correspond to ecological limits in brook trout, an iconic cold-water fish. Conserv Physiol 2015;3:cov017.
Musa N, Ramly HR, Manaf MTA et al. High water temperature impairs physiological responses in red hybrid tilapia: effects on cortisol and its regulation. Aquac Aquarium, Conserv Legis 2017;10:1297–308.
Valdivieso A, Ribas L, Piferrer F. Ovarian transcriptomic signatures of zebrafish females resistant to different environmental perturbations. J Exp Zool Part B Mol Dev Evol 2019;332: 55–68.
Hattori RS, Fernandino JI, Kishil A et al. Cortisol-induced masculinization: does thermal stress affect gonadal fate in pejerrey, a teleost fish with temperature-dependent sex determination?. PLoS One 2009;4.
Hayashi Y, Kobira H, Yamaguchi T et al. High temperature causes masculinization of genetically female medaka by elevation of cortisol. Mol Reprod Dev 2010;77:679–86.
Yamaguchi T, Yoshinaga N, Yazawa T et al. Cortisol is involved in temperature-dependent sex determination in the Japanese flounder. Endocrinology 2010;151:3900–8.
Fernandino JI, Hattori RS, Kishii A et al. The cortisol and androgen pathways cross talk in high temperature-induced masculinization: the 11$β$-hydroxysteroid dehydrogenase as a key enzyme. Endocrinology 2012;153:6003–11.
Fernandino JI, Hattori RS, Moreno Acosta OD et al. Environmental stress-induced testis differentiation: androgen as a by-product of cortisol inactivation. Gen Comp Endocrinol 2013;192:36–44.
Cortés DCC, Padilla LFA, Langlois VS et al. The central nervous system acts as a transducer of stress-induced masculinization through corticotropin-releasing hormone B. Development 2019;146:dev172866.
Nivelle R, Gennotte V, Kalala EJK et al. Temperature preference of Nile tilapia (Oreochromis niloticus) juveniles induces spontaneous sex reversal. PLoS One 2019;14:1–19.
Guerrero RD, Shelton WL. An aceto-carmine squash method for sexing juvenile fishes. N Am J Aquac 1974;36:56.
Conte MA, Gammerdinger WJ, Bartie KL et al. A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics 2017;18:1–19.
Dobin A, Davis CA, Schlesinger F et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15–21.
Andrews S. Babraham bioinformatics-FastQC a quality control tool for high throughput sequence data. Babraham Inst. 2010.
Ewels P, Magnusson M, Lundin S et al. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016;32:3047–8.
Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 2012;28:2184–5.
Law CW, Chen Y, Shi W et al. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 2014;15:1–17.
Ritchie ME, Phipson B, Wu DI et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015;43:e47.
Law CW, Monther A, Su S et al. Analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 3; referees: 3 approved] referee status. F1000Research 2018;5:1–29.
Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res 2019;47:e47.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26:139–40.
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008;9:1–13.
Csardi G, Nepusz T et al. The igraph software package for complex network research. InterJournal, Complex Syst 2006;1695:1–9.
Pedersen TL. Ggraph: an implementation of grammar of graphics for graphs and networks. 2020. https://cran.r-project.org/package=ggraph (11/23/2023).
Kanehisa M. Toward understanding the origin and evolution of cellular organisms. Protein Sci 2019;28:1947–51.
Kanehisa M, Furumichi M, Sato Y et al. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res 2021;49:D545–51.
Yu G, Wang LG, Han Y et al. ClusterProfiler: an R package for comparing biological themes among gene clusters. Omi A J Integr Biol 2012;16:284–7.
Agarwala R, Barrett T, Beck J et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2018;46:D.
Drost H-G, Paszkowski J, Hancock J. Biomartr: genomic data retrieval with R. Bioinformatics 2017;33:1216–7.
Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics 2013;29:1830–1.
Ashburner M, Ball CA, Blake JA et al. Gene ontology: tool for the unification of biology. Nat Genet 2000;25:25–9.
Mi H, Muruganujan A, Ebert D et al. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res 2019;47: D419–26.
Carbon S, Douglass E, Good BM. The Gene Ontology Consortium. The gene ontology resource: enriching a GOld mine. Nucleic Acids Res 2021;49:325–34.
Wickham H. ggplot2: Elegant Graphics for Data Analysis (Use R!). NY: Springer New York, 2010.