Alvarez M, Schrey AW, Richards CL. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Mol Ecol. 2015;24(4):710–25. https://doi.org/10.1111/mec.13055.
Article
CAS
PubMed
Google Scholar
Roberts WR, Roalson EH. Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). BMC Genomics. 2017;18(1):240.
Article
PubMed
PubMed Central
Google Scholar
Carruthers M, Yurchenko AA, Augley JJ, Adams CE, Herzyk P, Elmer KR. De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics. 2018;19(1):32.
Article
PubMed
PubMed Central
Google Scholar
Moreno-Santillán DD, Machain-Williams C, Hernández-Montes G, Ortega J. De novo transcriptome assembly and functional annotation in five species of bats. Sci Rep. 2019;9(1):6222.
Article
PubMed
PubMed Central
Google Scholar
Page TM, McDougall C, Diaz-Pulido G. De novo transcriptome assembly for four species of crustose coralline algae and analysis of unique orthologous genes. Sci Rep. 2019;9(1):12611.
Article
PubMed
PubMed Central
Google Scholar
Bay RA, Palumbi SR. Transcriptome predictors of coral survival and growth in a highly variable environment. Ecol Evol. 2017;7(13):4794–803. https://doi.org/10.1002/ece3.2685.
Article
PubMed
PubMed Central
Google Scholar
Kumaresan V, Nizam F, Ravichandran G, Viswanathan K, Palanisamy R, Bhatt P, et al. Transcriptome changes of blue-green algae, Arthrospira sp. in response to sulfate stress. Algal Res. 2017;23:96–103. https://doi.org/10.1016/j.algal.2017.01.012.
Article
Google Scholar
Watson H, Videvall E, Andersson MN, Isaksson C. Transcriptome analysis of a wild bird reveals physiological responses to the urban environment. Sci Rep. 2017;7(1):1–10.
Article
Google Scholar
Trego ML, Whitehead A, Kellar NM, Lauf M, Lewison RL. Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight. Conserv Physiol. 2019;7(1):coz018.
Article
PubMed
PubMed Central
Google Scholar
Morey JS, Neely MG, Lunardi D, Anderson PE, Schwacke LH, Campbell M, et al. RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins. BMC Genomics. 2016;17(1):720. https://doi.org/10.1186/s12864-016-3020-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morey JS, Burek Huntington KA, Campbell M, Clauss TM, Goertz CE, Hobbs RC, et al. De novo transcriptome assembly and RNA-Seq expression analysis in blood from beluga whales of Bristol Bay. AK Mar Genomics. 2017;35:77–92. https://doi.org/10.1016/j.margen.2017.08.001.
Article
PubMed
Google Scholar
Liew C-C, Ma J, Tang H-C, Zheng R, Dempsey AA. The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. J Lab Clin Med. 2006;147(3):126–32. https://doi.org/10.1016/j.lab.2005.10.005.
Article
CAS
PubMed
Google Scholar
Di Meo A, Bartlett J, Cheng Y, Pasic MD, Yousef GM. Liquid biopsy: a step forward towards precision medicine in urologic malignancies. Mol Cancer. 2017;16(1):80. https://doi.org/10.1186/s12943-017-0644-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caza F, de Boissel PGJ, Villemur R, Betoulle S, St-Pierre Y. Liquid biopsies for omics-based analysis in sentinel mussels. PLoS One. 2019;14(10):e0223525. https://doi.org/10.1371/journal.pone.0223525.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waits DS, Simpson DY, Sparkman AM, Bronikowski AM, Schwartz TS. The utility of reptile blood transcriptomes in molecular ecology. Mol Ecol Res. 2020;20(1):308.
Article
CAS
Google Scholar
Huang Z, Gallot A, Lao NT, Puechmaille SJ, Foley NM, Jebb D, et al. A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals. Mol Ecol Res. 2016;16(1):150–62. https://doi.org/10.1111/1755-0998.12447.
Article
CAS
Google Scholar
Chiari Y, Galtier N. RNA extraction from sauropsids blood: evaluation and improvement of methods. Amphib-Reptil. 2011;32(1):136–9. https://doi.org/10.1163/017353710X543010.
Article
Google Scholar
Townsend K, Ness J, Hoguet J, Stacy NI, Komoroske LK, Lynch JM. Testing the stability of plasma protein and whole blood RNA in archived blood of loggerhead sea turtles, Caretta caretta. Biopreserv Biobank. 2020;18(5):358.
Article
CAS
PubMed
Google Scholar
Komoroske LM, Jensen MP, Stewart KR, Shamblin BM, Dutton PH. Advances in the application of genetics in marine turtle biology and conservation. Front Mar Sci. 2017;4. https://doi.org/10.3389/fmars.2017.00156.
Hays GC, Hawkes LA. Satellite tracking sea turtles: opportunities and challenges to address key questions. Front Mar Sci. 2018;5. https://doi.org/10.3389/fmars.2018.00432.
IUCN. The IUCN Red List of Threatened Species. 2020. Available from: https://www.iucnredlist.org
Google Scholar
U.S. Fish & Wildlife Service. Summary of listed species and recovery plans—US Fish & Wildlife Service species reports. In: U.S. Fish and Wildlife Service, ECOS Environmental Conservation Online System. 2020; Available from: http://ecos.fws.gov/tess_public/pub/Boxscore.do
Google Scholar
Almpanidou V, Markantonatou V, Mazaris AD. Thermal heterogeneity along the migration corridors of sea turtles: implications for climate change ecology. J Exper Mar Biol Ecol. 2019;520:151223. https://doi.org/10.1016/j.jembe.2019.151223.
Article
Google Scholar
Chaloupka M, Balazs GH, Work TM. Rise and fall over 26 years of a marine epizootic in Hawaiian green sea turtles. J Wildl Dis. 2009;45(4):1138–42. https://doi.org/10.7589/0090-3558-45.4.1138.
Article
PubMed
Google Scholar
Clukey KE, Lepczyk CA, Balazs GH, Work TM, Li QX, Bachman MJ, et al. Persistent organic pollutants in fat of three species of Pacific pelagic longline caught sea turtles: accumulation in relation to ingested plastic marine debris. Sci Tot Environ. 2018;610–611:402–11.
Article
Google Scholar
Jensen MP, Allen CD, Eguchi T, Bell IP, LaCasella EL, Hilton WA, et al. Environmental warming and feminization of one of the largest sea turtle populations in the world. Curr Biol. 2018;28(1):154–159.e4.
Article
CAS
PubMed
Google Scholar
Work TM, Balazs GH. Pathology and distribution of sea turtles landed as bycatch in the Hawaii-based North Pacific pelagic longline fishery. J Wildl Dis. 2010;46(2):422–32. https://doi.org/10.7589/0090-3558-46.2.422.
Article
PubMed
Google Scholar
Naro-Maciel E, Le M, FitzSimmons NN, Amato G. Evolutionary relationships of marine turtles: a molecular phylogeny based on nuclear and mitochondrial genes. Mol Phylogenet Evol. 2008;49(2):659–62. https://doi.org/10.1016/j.ympev.2008.08.004.
Article
CAS
PubMed
Google Scholar
Bostrom BL, Jones TT, Hastings M, Jones DR. Behaviour and physiology: the thermal strategy of leatherback turtles. PLoS One. 2010;5(11):e13925. https://doi.org/10.1371/journal.pone.0013925.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wyneken J. Anatomy of the leatherback turtle. In: The Leatherback Turtle: Biol and Conservation: Johns Hopkins University Press; 2015. p. 32–48.
Duchene S, Frey A, Alfaro-Núñez A, Dutton PH, Thomas P, Gilbert M, et al. Marine turtle mitogenome phylogenetics and evolution. Mol Phylogenet Evol. 2012;65(1):241–50. https://doi.org/10.1016/j.ympev.2012.06.010.
Article
PubMed
Google Scholar
Pereira AG, Sterli J, Moreira FRR, Schrago CG. Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles. Mol Phylogenet Evol. 2017;113:59–66. https://doi.org/10.1016/j.ympev.2017.05.008.
Article
PubMed
Google Scholar
Avise JC, Bowen BW, Lamb T, Meylan AB, Bermingham E. Mitochondrial DNA evolution at a turtle’s pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines. Mol Biol Evol. 1992;9(3):457–73. https://doi.org/10.1093/oxfordjournals.molbev.a040735.
Article
CAS
PubMed
Google Scholar
Komoroske LM, Miller MR, O’Rourke SM, Stewart KR, Jensen MP, Dutton PH. A versatile rapture (RAD-capture) platform for genotyping marine turtles. Mol Ecol Res. 2019;19(2):497–511. https://doi.org/10.1111/1755-0998.12980.
Article
Google Scholar
Martínez-Fernández M, Bernatchez L, Rolán-Alvarez E, Quesada H. Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis. BMC Evol Biol. 2010;10(1):356. https://doi.org/10.1186/1471-2148-10-356.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kenkel CD, Matz MV. Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nat Ecol Evol. 2016;1(1):1–6.
Google Scholar
Seminoff JA, Allen CD, Balazs GH, Dutton PH, Eguchi T, Haas HL, et al. Status review of the green turtle (Chelonia mydas) under the Endangered Species Act. NOAA Tech Memor NOAA-NMFS-SWFSC-539; 2015. p. 571.
Google Scholar
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–6. https://doi.org/10.1093/bioinformatics/bti610.
Article
CAS
PubMed
Google Scholar
Kanehisa M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 2019;28(11):1947–51. https://doi.org/10.1002/pro.3715.
Article
CAS
PubMed
PubMed Central
Google Scholar
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):1.
Article
Google Scholar
Akbarzadeh A, Günther OP, Houde AL, Li S, Ming TJ, Jeffries KM, et al. Developing specific molecular biomarkers for thermal stress in salmonids. BMC Genomics. 2018;19(1):749. https://doi.org/10.1186/s12864-018-5108-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller KM, Günther OP, Li S, Kaukinen KH, Ming TJ. Molecular indices of viral disease development in wild migrating salmon. Conserv Physiol. 2017;5(1):cox036.
Article
PubMed
PubMed Central
Google Scholar
Yadetie F, Karlsen OA, Lanzén A, Berg K, Olsvik P, Hogstrand C, et al. Global transcriptome analysis of Atlantic cod (Gadus morhua) liver after in vivo methylmercury exposure suggests effects on energy metabolism pathways. Aquat Toxicol. 2013;126:314–25. https://doi.org/10.1016/j.aquatox.2012.09.013.
Article
CAS
PubMed
Google Scholar
Trego ML, Hoh E, Whitehead A, Kellar NM, Lauf M, Datuin DO, et al. Contaminant exposure linked to cellular and endocrine biomarkers in Southern California bottlenose dolphins. Environ Sci Technol. 2019;53(7):3811–22. https://doi.org/10.1021/acs.est.8b06487.
Article
CAS
PubMed
Google Scholar
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–512. https://doi.org/10.1038/nprot.2013.084.
Article
CAS
PubMed
Google Scholar
Freedman AH, Clamp M, Sackton TB. Error, noise and bias in de novo transcriptome assemblies. Mol Ecol Res. 2021;21(1):18–29. https://doi.org/10.1111/1755-0998.13156.
Article
CAS
Google Scholar
Bentley BP, Haas BJ, Tedeschi JN, Berry O. Loggerhead Sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress. Mol Ecol. 2017;26(11):2978–92. https://doi.org/10.1111/mec.14087.
Article
CAS
PubMed
Google Scholar
Lübbe A, Schaffner W. Tissue-specific gene expression. Trends Neurosci. 1985;8:100–4. https://doi.org/10.1016/0166-2236(85)90046-3.
Article
Google Scholar
Sonawane AR, Platig J, Fagny M, Chen C-Y, Paulson JN, Lopes-Ramos CM, et al. Understanding tissue-specific gene regulation. Cell Rep. 2017;21(4):1077–88. https://doi.org/10.1016/j.celrep.2017.10.001.
Article
CAS
PubMed
PubMed Central
Google Scholar
Telemeco RS, Simpson DY, Tylan C, Langkilde T, Schwartz TS. Contrasting responses of lizards to divergent ecological stressors across biological levels of organization. Integr Comp Biol. 2019;59(2):292–305. https://doi.org/10.1093/icb/icz071.
Article
CAS
PubMed
Google Scholar
Byrne A, Supple MA, Volden R, Laidre KL, Shapiro B, Vollmers C. Depletion of hemoglobin transcripts and long-read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus). Front Genet. 2019;10. https://doi.org/10.3389/fgene.2019.00643.
Westermann AJ, Gorski SA, Vogel J. Dual RNA-seq of pathogen and host. Nat Rev Microbiol. 2012;10(9):618–30. https://doi.org/10.1038/nrmicro2852.
Article
CAS
PubMed
Google Scholar
Lehman BM, Johnson RC, Adkison M, Burgess OT, Connon RE, Fangue NA, et al. Disease in central valley salmon: status and lessons from other systems. San Francisco Estuary Watershed Sci. 2020;18(3):1–31. https://doi.org/10.15447//SFEWS.2020V18ISS3ART2.
Santos JC, Tarvin RD, O’Connell LA, Blackburn DC, Coloma LA. Diversity within diversity: parasite species richness in poison frogs assessed by transcriptomics. Mol Phylogenet Evol. 2018;125:40–50. https://doi.org/10.1016/j.ympev.2018.03.015.
Article
CAS
PubMed
Google Scholar
Larsen PA, Hayes CE, Williams CV, Junge RE, Razafindramanana J, Mass V, et al. Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar’s lemurs. Biol Lett. 2016;12(1):20150829. https://doi.org/10.1098/rsbl.2015.0829.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu G, Zhang H, Sun G, Zhao C, Shang S, Gao X, et al. Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus). BMC Genomics. 2017;18(1):584. https://doi.org/10.1186/s12864-017-3983-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
McGaugh SE, Bronikowski AM, Kuo C-H, Reding DM, Addis EA, Flagel LE, et al. Rapid molecular evolution across amniotes of the IIS/TOR network. PNAS. 2015;112(22):7055–60. https://doi.org/10.1073/pnas.1419659112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Griffiths JS, Pan T-CF, Kelly MW. Differential responses to ocean acidification between populations of Balanophyllia elegans corals from high and low upwelling environments. Mol Ecol. 2019;28:2715.
CAS
PubMed
Google Scholar
Whitehead A, Crawford DL. Variation in tissue-specific gene expression among natural populations. Genome Biol. 2005;6(2):R13. https://doi.org/10.1186/gb-2005-6-2-r13.
Article
PubMed
PubMed Central
Google Scholar
Schoville SD, Barreto FS, Moy GW, Wolff A, Burton RS. Investigating the molecular basis of local adaptation to thermal stress: population differences in gene expression across the transcriptome of the copepod Tigriopus californicus. BMC Evol Biol. 2012;12(1):170. https://doi.org/10.1186/1471-2148-12-170.
Article
CAS
PubMed
PubMed Central
Google Scholar
Garcia TI, Shen Y, Crawford D, Oleksiak MF, Whitehead A, Walter RB. RNA-Seq reveals complex genetic response to Deepwater horizon oil release in Fundulus grandis. BMC Genomics. 2012;13(1):474. https://doi.org/10.1186/1471-2164-13-474.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cortés-Gómez AA, Morcillo P, Guardiola FA, Espinosa C, Esteban MA, Cuesta A, et al. Molecular oxidative stress markers in olive ridley turtles (Lepidochelys olivacea) and their relation to metal concentrations in wild populations. Environ Pollut. 2018;233:156–67. https://doi.org/10.1016/j.envpol.2017.10.046.
Article
CAS
PubMed
Google Scholar
Cocci P, Mosconi G, Bracchetti L, Nalocca JM, Frapiccini E, Marini M, et al. Investigating the potential impact of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on gene biomarker expression and global DNA methylation in loggerhead sea turtles (Caretta caretta) from the Adriatic Sea. Sci Tot Environ. 2018;619–620:49–57.
Article
Google Scholar
Lehnert K, Siebert U, Reißmann K, Bruhn R, McLachlan MS, Müller G, et al. Cytokine expression and lymphocyte proliferative capacity in diseased harbor porpoises (Phocoena phocoena) – biomarkers for health assessment in wildlife cetaceans. Environ Pollut. 2019;247:783–91. https://doi.org/10.1016/j.envpol.2019.01.079.
Article
CAS
PubMed
Google Scholar
Van Houtan KS, Hargrove SK, Balazs GH. Land use, macroalgae, and a tumor-forming disease in marine turtles. Thrush S, editor. PLoS One. 2010;5(9):e12900.
Article
PubMed
PubMed Central
Google Scholar
Aguirre AA, Lutz PL. Marine turtles as sentinels of ecosystem health: is fibropapillomatosis an indicator? EcoHealth. 2004;1(3):275.
Google Scholar
Work TM. Cancer in sea turtles. Hawaii Med J. 2005;64:23–4. https://core.ac.uk/download/pdf/77122956.pdf.
Hargrove SA, Work TM, Brunson S, Foley AM, Balazs GH. Proceedings of the 2015 international summit on fibropapillomatosis : global status, trends, and population impacts. NOAA Technical Memorandum NMFS-PIFSC-54; 2016.
Google Scholar
Jensen MP, FitzSimmons NN, Bourjea J, Hamabata T, Reece J, Dutton PH. The evolutionary history and global phylogeography of the green turtle (Chelonia mydas). J Biogeogr. 2019;46(5):860–70. https://doi.org/10.1111/jbi.13483.
Article
Google Scholar
Komoroske LM, Lewison RL, Seminoff JA, Deheyn DD, Dutton PH. Pollutants and the health of green sea turtles resident to an urbanized estuary in San Diego. CA Chemosphere. 2011;84(5):544–52. https://doi.org/10.1016/j.chemosphere.2011.04.023.
Article
CAS
PubMed
Google Scholar
Balazs GH, Parker DM. Ocean pathways and residential foraging locations for satellite tracked green turtles breeding at French Frigate Shoals in the Hawai’ian Islands. Micronesica. 2017;4:1.
Google Scholar
Bennett P, Keuper-Bennett U, Balazs GH. Remigration and residency of Hawaiian green turtles in coastal waters of Honokowai, West Maui, Hawaii. Proceedings of the Twentieth Annual Symposium on Sea Turtle Biology and Conservation US Dept Commerce, NOAA Tech Memo NMFS-SEFSC-477; 2002. p. 289290.
Google Scholar
Greytak SR, Champlin D, Callard GV. Isolation and characterization of two cytochrome P450 aromatase forms in killifish (Fundulus heteroclitus): differential expression in fish from polluted and unpolluted environments. Aquat Toxicol. 2005;71(4):371–89. https://doi.org/10.1016/j.aquatox.2004.12.007.
Article
CAS
PubMed
Google Scholar
Jeffries KM, Hinch SG, Gale MK, Clark TD, Lotto AG, Casselman MT, et al. Immune response genes and pathogen presence predict migration survival in wild salmon smolts. Mol Ecol. 2014;23(23):5803–15. https://doi.org/10.1111/mec.12980.
Article
CAS
PubMed
Google Scholar
Pujade Busqueta L, Crocker DE, Champagne CD, McCormley MC, Deyarmin JS, Houser DS, et al. A blubber gene expression index for evaluating stress in marine mammals. Conserv Physiol. 2020;8(1):coaa082.
Article
PubMed
PubMed Central
Google Scholar
Allen CD, Robbins MN, Eguchi T, Owens DW, Meylan AB, Meylan PA, et al. First assessment of the sex ratio for an East Pacific green sea turtle foraging aggregation: validation and application of a testosterone ELISA. PLoS One. 2015;10(10):e0138861. https://doi.org/10.1371/journal.pone.0138861.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tezak B, Sifuentes-Romero I, Milton S, Wyneken J. Identifying sex of neonate turtles with temperature-dependent sex determination via small blood samples. Sci Rep. 2020;10(1):5012. https://doi.org/10.1038/s41598-020-61984-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Owens DW, Ruiz GJ. New methods of obtaining blood and cerebrospinal fluid from marine turtles. Herpetologica. 1980;36(1):17–20.
Google Scholar
Komoroske LM. NEB directional kit working RNA-sequencing library preparation protocol. Available from: https://github.com/MolEcolConsLab/Wet-Lab-Protocols/blob/master/NEBdirectionalkit.working. SOP.Komoroske.lab_JP_LK_SB.docx.
Buffalo V. Scythe – a Bayesian adapter trimmer [internet]. 2014. Available from: https://github.com/vsbuffalo/scythe
Google Scholar
Joshi J, Fass J. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files. Available from: https://github.com/najoshi/sickle
DeBiasse MB, Kawji Y, Kelly MW. Phenotypic and transcriptomic responses to salinity stress across genetically and geographically divergent Tigriopus californicus populations. Mol Ecol. 2018;27(7):1621–32. https://doi.org/10.1111/mec.14547.
Article
CAS
PubMed
Google Scholar
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet. 2013;45(6):701–6. https://doi.org/10.1038/ng.2615.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–52. https://doi.org/10.1038/nbt.1883.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smith-Unna R, Boursnell C, Patro R, Hibberd JM, Kelly S. TransRate: reference-free quality assessment of de novo transcriptome assemblies. Genome Res. 2016;26(8):1134–44. https://doi.org/10.1101/gr.196469.115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2. https://doi.org/10.1093/bioinformatics/bts565.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417–9. https://doi.org/10.1038/nmeth.4197.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brown CT. gather-counts.py. 2015. Available from: https://github.com/dib-lab/2017-dibsi-metagenomics/blob/master/gather-counts.py
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40. https://doi.org/10.1093/bioinformatics/btp616.
Article
CAS
PubMed
Google Scholar
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2. https://doi.org/10.1093/bioinformatics/btv351.
Article
CAS
PubMed
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60. https://doi.org/10.1038/nmeth.3176.
Article
CAS
PubMed
Google Scholar
Demasius W, Weikard R, Hadlich F, Müller KE, Kühn C. Monitoring the immune response to vaccination with an inactivated vaccine associated to bovine neonatal pancytopenia by deep sequencing transcriptome analysis in cattle. Vet Res. 2013;44(1):93. https://doi.org/10.1186/1297-9716-44-93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Correia CN, McLoughlin KE, Nalpas NC, Magee DA, Browne JA, Rue-Albrecht K, et al. RNA sequencing (RNA-Seq) reveals extremely low levels of reticulocyte-derived globin gene transcripts in peripheral blood from horses (Equus caballus) and cattle (Bos taurus). Front Genet. 2018;9. https://doi.org/10.3389/fgene.2018.00278.
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas B, Papanicolaou A. Transdecoder (find coding regions within transcripts) [internet]. 2018. Available from: http://transdecoder.sf.net
Google Scholar
R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020.
Google Scholar
Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017;33(18):2938–40. https://doi.org/10.1093/bioinformatics/btx364.
Article
CAS
PubMed
PubMed Central
Google Scholar
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functional annotation and data mining with the Blast2GO suitec. Nucleic Acids Res. 2008;36(10):3420.
Article
PubMed
PubMed Central
Google Scholar
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47(D1):D309–14. https://doi.org/10.1093/nar/gky1085.
Article
CAS
PubMed
Google Scholar
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. https://doi.org/10.1093/nar/gkv007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alexa A, Rahnenfuhrer J. topGO: enrichment analysis for gene ontology; 2019.
Google Scholar
Alexa A, Rahnenfuhrer J. Gene set enrichment analysis with topGO. 2020. https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
Google Scholar
Walter W, Sánchez-Cabo F, Ricote M. GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics. 2015;31(17):2912–4. https://doi.org/10.1093/bioinformatics/btv300.
Article
CAS
PubMed
Google Scholar