Abdellaoui N., Kim M. J., Choi T. J. (2019) Transcriptome analysis of gene expression in Chlorella vulgaris under salt stress. World J. Microbiol. Biotechnol. 35: 141 doi.org/10.1007/s11274-019-2718-6 Aguilar-Díaz H., Carrero J. C., Argüello-García R., Laclette J. P., Morales-Montor J. (2011) Cyst and encystment in protozoan parasites: optimal targets for new life-cycle interrupting strategies? Trends Parasitol. 27: 450–458 Anderson O. R. (2011) Particle-associated planktonic naked amoebae in the Hudson Estuary: Size-fraction related densities, cell sizes and estimated carbon content. Acta Protozool. 50: 315–22 Anderson O. R. (2014) Living together in the plankton: A survey of marine protist symbioses. Acta Protozool. 53: 29–38 Arora N., Pienkos P. T., Pruthi V., Poluri K. M., Guranieri M. T. (2018) Leveraging algal omics to reveal potential targets for augmenting TAG accumulation. Biotechnol. Adv. 36: 1274–1292 Ashworth J., Coesel S., Lee A., Armbrust E. V., Orellana M. V., Baliga N. S. (2013) Genome- wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc. Natl. Acad. Sci. U.S.A. 110: 7518–7523 Azaman S. N. A., Wong D. C. J., Tan S. W., Yusoff F. M., Nagao N., Yeap S. K. (2020) De denovo transcriptome analysis of Chlorella sorokiniana: Effect of glucose assimilation, and moderate light intensity. Sci. Rep. 10: 17331 https://doi.org/10.1038/s41598-020-74410-4 Barrantes I., Glöckner G., Meyer S., Marwan W. (2010) Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum. BMC Genom. 11: 115 http://www.biomedcentral.com/1471-2164/11/115 Barrartt J. L. N., Cao M., Stark D. J., Ellis J. T. (2015) The transcriptome sequence of Dientamoeba fragilis offers new biological insights on its metabolism, kinome, degradome and potential mechanisms of pathogenicity. Protist 166: 389–408 Baumel-Alterzon S., Ankri S. (2014) Entamoeba histolytica adaptation to glucose starvation: A matter of life and death. Curr. Opin. Microbiol. 20: 139–145 Beinart R. A., Beaudoin D. J., Benhard J. M., Edgcomb V. P. (2018) Insights into the metabolic functioning of a multipartner ciliate symbiosis from oxygen-depleted sediments. Mol. Ecol. 27: 1794-1807 DOI: 10.1111/mec.14465 Beisser D., Graupner N., Bock C., Wodniok S., Grossmann L., Vos M., Sures B., Rahmann S., Boenigk J. (2017) Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes. PeerJ. 5: e2832 DOI:10.7717/peerj.2832 Belew A. T., Junqueira C., Rogrigues-Luiz G. F., Valente B. M., Oliveira A. E. R., Polidoro R. B., Zuccherato L. W., Bartholomeu D. C., Schenkman S., Gazzinelli R. T., Burleigh B. A., El-Sayed N. M., Teixeira S. M. R. (2017) Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection. PLOS Pathog. 13(12): e1006767. https://doi.org/10.1371/journal.ppat.1006767 Beszteri S., Thomas S., Benes V., Harms L., Trimborn S. (2018) The response of three southern ocean phytoplankton species to ocean acidification and light availability: A transcriptomic study. Protist 169: 958–975 Blicke G., Osuna-Cruz C. M., Silva M. S., Poulsen N., D’hondt S., Bulankova P., Vyverman W., De Veylder L., Vandepoele K. (2021) Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. Plant J. 107: 315–336 Bonkowski M., Clarholm M. (2012) Stimulation of plant growth through interactions of bacteria and protozoa: Testing the auxiliary microbial loop hypothesis. Acta Protozool. 51: 237–247 Bozdech Z., Llinás M., Pulliam B. L., Wong E. D., Zhu J., DeRisi J. L. (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLOS Biol. 1: 085-099 DOI: 10.1371/journal.pbio.0000005 Burns J. A., Paasch A., Narechania A., Kim E. (2015) Comparative genomics of a bacterivorous green alga reveals evolutionary causalities and consequences of phago-mixotrophic mode of nutrition. Genome Biol. Evol. 7: 3047–3061 Burns J. A., Zhang H., Hill E., Kim E., Kerney R. (2017) Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis. eLIFE 6: e22054. DOI: 10.7554/eLife.22054 Bussard A., Corre E., Hubas C., Duvernois-Berthet E., Le Corguillé G., Jourdren L., Coulpier F., Claquin P., Lopez P. J. (2017) Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms. Environ. Microbiol. 19: 909– 925 Caron D. A. (2005) Marine microbial ecology in a molecular world: What does the future hold? Sci. Mar. 69: 97–110 Caron D. A., Alexander H., Allen A. E., Archibald J. M., Armbrust E. V., Bachy C., Bell C. J., Bharti A., Dyhrman S. T., Guida S. M., Heidelberg K. B, Kaye J. Z., Metzner J., Smith S. R., Worden A. Z. (2017) Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat. Rev. Microbiol. 15: 6–20 Carradec Q., Pelletier E., Da Silva C., Alberti A., Seeleuthner Y., Blanc-Mathieu R. et al. (2018). A global ocean atlas of eukaryotic genes. Nature communications 9: 1–13 Chang W.-C., Zheng H.-Q., Chen C.-N. N. (2016) Comparative transcriptome analysis reveals a potential photosynthate partitioning mechanism between lipid and starch biosynthetic pathways in green microalgae. Algal Res. 16: 54–62 Cheng R., Feng J., Zhang B.-X., Huang Y., Cheng J., Zhang C.-X. (2014) Transcriptome and gene expression analysis of an oleaginous diatom under different salinity conditions. Bioenerg. Res. 7: 192–205 Crotty F. V., Adl S. M., Blackshaw R. P., Murray P. J. (2012) Protozoan pulses unveil their pivotal position within the soil food web. Microb. Ecol. 63: 905–918 De Cádiz A. E., Jeelani G., Nakada-Tsukui K., Caler E., Nozaki T. (2013) Transcriptome analysis of encystation in Entamoeba invadens. PLOS One 8(9): e74840 DOI:10.137/journal.pone.0074840 De Ruiter P. C., Neutel A.-M., Moore J. C. (1995) Energetics, patterns of interaction strengths, and stability in real ecosystems. Science 269: 1257–1260 De Vries J., de Vries S., Curtis B. A., Zhou H., Penny S., Feussner K., Pinto D. M., Steinert M., Cohen A. M., von Schwartzenberg K., Archibald J. M. (2020) Heat stress response in the closest algal relatives of land plants reveals conserved stress signaling circuits. Plant J. 103: 1025–1048 Dohra H., Fujishima M., Suzuki H. (2015) Analysis of amino acid and codon usage in Paramecium bursaria. FEBS Lett. 589: 3113–3118 Dos Santos C. M. B., Ludwig A., Kessler R. L., Rampazzo R. C. P., Inoue A. H., Krieger M. A., Pavoni D. P., Probst C. M. (2018) Trypanosoma cruzi transcriptome during axenic epimastigote growth curve. Mem. Inst. Oswaldo Cruz, Rio de Janeiro, 113(5): e170404 DOI: 10.1590/0074-02760170404 Ehrenkaufer G. M., Weedall G. D., Williams D., Lorenzi H. A., Caler E., Hall N., Singh U. (2013) The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation. Genome Biol. 14: R77 http://genomebiology.com/2013/14/7/R77 Einarsson E., Troell K., Hoeppner M. P., Grabherr M., Ribacke U., Svärd S. G. (2016) Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis. PLoS Negl. Trop. Dis. 10(3): e0004571. DOI:10.1371/journal.pntd.0004571 Faghiri Z., Widmer G. (2011) A comparison of the Giardia lamblia trophozoite and cyst transcriptome using microarrays. BMC Microbiol. 11: 91 http://www.biomedcentral.com/1471-2180/11/91 Fan M., Sun X., Xu N., Liao Z., Li Y., Wang J., Fan Y., Cui D., Li P., Miao Z. (2017) Integration of deep transcriptome and proteome analyses of salicylic acid regulation high temperature stress in Ulva prolifera. Sci. Rep. 7: 11052 DOI:10.1038/s41598-017-11449-w Fang L., Qi S., Xu Z., Wang W., He J., Chen X., Liu J. (2017) De novo transcriptomic profiling of Dunaliella salina reveals concordant flows of glycerol metabolic pathways upon reciprocal salinity changes. Algal Res. 23: 135–149 Feng J.-M., Jiang C.-Q., Sun Z.-Y., Hua C.-J., Wen J.-F., Miao W., Xiong J. (2020) Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment. Mol. Phylogenet. Evol. 143: 106687 https://doi.org/10.1016/j.ympev.2019.106687 Fujiwara T., Hirooka S., Ohbayashi R., Onuma R., Miyagishima S. (2020) Relationship between cell cycle and diel transcriptomic changes in metabolism in a unicellular red alga. Plant Physiol. 183: 1484–1501 Gao X., Cong Y., Yue J., Xing Z., Wang Y., Chai X. (2019) Small RNA, transcriptome, and degradome sequencing to identify salinity stress responsive miRNAs and target genes in Dunaliella salina. J. Appl. Phycol. 31: 1175–1183 Garcia-Jiménez P., Robaina R. R. (2015) On reproduction in red algae: Further research needed at the molecular level. Front. Plant Sci. 6: 93 doi: 10.3389/fpls.2015.00093 Garcia-Jiménez P., Llorens C., Roig F. J., Robaina R. R. (2018) Analysis of the transcriptome of the red seaweed Grateloupia imbricata with emphasis on reproductive potential. Mar. Drugs 16: 490 doi:10.3390/md16120490 Geisen S., Tveit A. T., Clark I. M., Richter A., Svenning M. M., Bonkowski M., Urich T. (2015) Metatranscriptomic census of active protists in soils. ISMEJ (2015) 9: 2178–2190 DOI:10.1038/ismej.2015.30 Gerber T., Loureiro C., Schramma N., Chen S., Jain A., Weber A., Weigert A., Santel M., Alim K., Treutlein B., Camp J. G. (2021) Nuclei are mobile processors enabling specialization in a gigantic single-celled syncytium BioRxiv. https://doi.org/10.1101/2021.04.29.441915 Gierz S. L., Foret S., Leggat W. (2017) Transcriptomic analysis of thermally stressed Symbiodinium reveals differential expression of stress and metabolism genes. Front. Plant Sci. 8: 271. doi: 10.3389/fpls.2017.00271 Gilchrist C. A., Petri, W. A. Jr. (2008) Using differential gene expression to study Entamoeba histolytica pathogenesis. Trends Parasitol. 25: 124–131. Glöckner G., Golderer G., Werner-Felmayer G., Meyer S., Marwan W. (2008) A first glimpse at the transcriptome of Physarum polycephalum. BMC Genom. 9: 6 http://www.biomedcentral.com/1471-2164/9/6 Gomaa F., Utter D. R., Powers C., Beaudoin D. J., Edgcomb V. P., Filipsson H. L., Hansel C. M., Wankel S. D., Zhang Y., Bernhard J. M. (2021) Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. Sci. Adv. 7: eabf1586 DOI: 10.1126/sciadv.abf1586 Guarnieri M. T., Pienkos P. T. (2015) Algal omics: Unlocking bioproduct diversity in algae cell factories. Photosynth. Res. 123: 255–263 Guo L., Yang G. (2015) The mechanism of the acclimation of Nannochloropsis oceanica to freshwater deduced from its transcriptome profiles. J. Ocean Univ. China 14: 922–930 Harding T., Brown M. W., Simpson A. G. B., Roger A. J. (2016) Osmoadaptative strategy and its molecular signature in obligately halophilic heterotrophic protists. Genome Biol. Evol. 8: 2241–2258 DOI:10.1093/gbe/evw152 Harke M. J., Juhl A. R., Haley S. T., Alexander H., Dyhrman S. T. (2017) Conserved transcriptional responses to nutrient stress in bloom-forming algae. Front. Microbiol. 8.1279 DOI: 10.3389/ fmicb.2017.01279 Hasni I., Decloquement P., Demanéche S., Mameri R. M., Abbe O., Colson P., La Scola B. (2020) Insight into the lifestyle of amoeba Willaertia magna during bioreactor growth using transcriptomics and proteomics. Microorganisms 2020 8: 771 DOI:10.3390/ microorganisms8050771 Hennon G. W. M., Limón M. D. H., Haley S. T., Juhl A. R., Dyhrman S. T. (2017) Diverse CO2-induced responses in physiology and gene expression among eukaryotic phytoplankton. Front. Microbiol. 8.2547 DOI: 10.3389/fmicb.2017.02547 Hines H. N., Onsbring H., Ettema T. J. G., Esteban G. F. (2018) Molecular investigation of the ciliate Spirostomum semivirescens, with first transcriptome and new geographical records. Protist 169: 875–886 Howick V. M., Russell A. J. C., Andrews T., Heaton H., Reid A. J., Natarajan K., Butungi H., Metcalf T., Verzier L. H., Rayner J. C., Berriman M., Herren J. K., Billker O., Hemberg M., Talman A. M., Lawniczak M. K. N. (2019) The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle. Science 365: eaaw2619 (2019) DOI: 10.1126/science.aaw2619 Hovde B. T., Dodato C. R., Hunsperger H. M., Ryken S. A., Yost W., Jha R. K., Patterson J., Monat R. J. Jr., Barlow S. B., Starkenburg S. R., Cattolico R. A. (2015) Genome sequence and transcriptome analyses of Chrysohromulina tobiin: Metabolic tools for enhanced algal fitness in the prominent order Prymnesiales (Haptophyceae). PLoS Genet. 11(9): e1005469. doi:10.1371/journal.pgen.1005469 Hu C., Cui D., Sun X., Shi J., Xu N. (2020) Primary metabolism is associated with the astaxanthin biosynthesis in the green algae Haematococcus pluvialis under light stress. Algal Res. 46: 101768 https://doi.org/10.1016/j.algal.2019.101768 Huang K.-Y., Shin J.-W., Huang P.-J., Ku F.-M., Lin W.-C., Lin R., Hsu W.-M., Tang P. (2013) Functional profiling of the Tritrichomonas foetus transcriptome and proteome. Mol. Biochem. Parasitol. 187: 60–71 Huang W., Ye J., Zhang J., Lin Y., He M., Huang J. (2016) Transcriptome analysis of Chlorella zofingiensis to identify genes and their expressions involved in astaxanthin and triacylglycerol biosynthesis. Algal Res. 17: 236–243 Huang L., Gao B., Wu M., Wang F., Zhang C. (2019) Comparative transcriptome analysis of a long-time span two-step culture process reveals a potential mechanism for astaxanthin and biomass hyper-accumulation in Haematococcus pluvialis JNU35. Biotechnol. Biofuels 12: 18 https://doi.org/10.1186/s13068-019-1355-5 Huang L., Peng L., Yan X. (2021) Multi-omics responses of red algae Pyropia haitanensis to intertidal desiccation during low tides. Algal Res. 58: 102376 https://doi.org/10.1016/J.algal.2021.102376 Husain A., Jeelani G., Sato D., Nozaki T. (2011) Global analysis of gene expression in response to L-cysteine deprivation in the anaerobic protozoan parasite Entamoeba histolytica. BMC Genomics 12: 275 http://www.biomedcentral.com/1471-2164/12/275 Hwang Y., Jung G., Jin E. (2008) Transcriptome analysis of acclimatory responses to thermal stress in Antarctic algae. Biochem. Biophys. Res. Commun. 367: 635–641 Inbar E., Hughitt V. K., Dillon L. A. L., Ghosh K., El-Sayed N. M., Sacks D. L. (2017) The transcriptome of Leishmania major developmental stages in their natural sand fly vector. MBio 8: e00029-17 https://doi.org/10.1128/mBio00029-17 Jeelani G., Sato D., Husain A., Cádiz A. E., Sugimoto M., Soga T., Suematsu M., Nozaki T. (2012) Metabolic profiling of the protozoan parasite Entamoeba invadens revealed activation of unpredicted pathway during encystation. PLoS ONE 7(5): e37740 DOI:10.1371/journal.pone.0037740 Jiang C., Wei W., Yan G., Shi T., Miao W. (2019) Transcriptome analysis reveals the molecular mechanism of resting cyst formation in Colpoda aspera. J. Eukaryot. Microbiol. 66: 212– 220 Kaiser K., Matuschewski K., Camargo N., Ross J., Kappe S. H. I. (2004) Differential transcriptome profiling identifies Plasmodium genes encoding pre-erythrocytic stage-specific proteins. Mol. Microbiol. 51: 1221–1232 Keeling P. J., Burki F., Wilcox H. M., Allam, B., Allen E. E., Amaral-Zettler L. A. et al. (2014) The Marine Microbial Eukaryote Transcriptome Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the ocean through transcriptome sequencing. PLoS Biol. 12(6): e1001889 DOI: 10.1371/journal.pbio.1001889 Klein B., Wibberg D., Hallmann A. (2017) Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. BMC Biol. 15: 111 DOI: 10.1186/s12915-017-0450-y Kodama Y., Suzuki H., Dohra H., Sugii M., Kitazume T., Yamaguchi K., Shigenobu S., Fujishima M. (2014) Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts. BMC Genomics 2014, 15: 183 http://www.biomedcentral.com/1471-2164/15/183 Krabberød A. K., Bjorbaekmo M. F. M., Shalchian-Tabrizi K., Logares R. (2017) Exploring the oceanic microeukaryotic interactome with metaomics approaches. Aquat. Microb. Ecol. 79: 1-12 https://doi.org/10.3354/ame01811 Ku C., Sebé-Pedrós A. (2019) Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes. Phil. Trans. R. Soc. B 374: 20190098 http://dx.doi.org/10.1098/rstb.2019.0098 Ku C., Sheyn U., Sebé-Pedrós A. Ben-Dor S., Schatz D., Tanay A., Rosenwasser S., Vardi A. (2020) A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. Sci Adv. 6: eaba4137 Labarre A., Obiol A., Wilken S., Forn I., Massana R. (2019) Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates. Limonol. Oceanogr. 65: S149-S160 Lhee D., Lee J., Ettahi K., Cho C.-H., Ha J.-S., Chan Y.-F., Zelzion U., Stephens T. G., Price D. C., Gabr A., Nowack E. C. M., Bhattacharya D., Yoon H. S. (2020) Amoeba genome reveals dominant host contribution to plastid endosymbiosis. Mol. Biol. Evol. 38: 344–357 Li Q., Zhang L., Liu J. (2019a) Comparative transcriptome analysis at seven time points during Haematococcus pluvialis motile cell growth and astaxanthin accumulation. Aquaculture 503: 304–311 Li Y., Gu W., Huang A., Xie X., Wu S., Wang G. (2019b) Transcriptome analysis reveals regulation of gene expression during photoacclimation to high irradiance levels in Dunaliella salina (Chlorophyceae). Phycological Res. 67: 291–302 Li L., Zhang X., He N., Wang X., Zhu P., Ji Z. (2019c) Transcriptome profiling of the salt-stress response in the halophytic green alga Dunaliella salina. Plant Mol. Biol. Rep. 37: 421–435 Li T., Yang F., Xu J., Wu H., Mo J., Dai L., Xiang W. (2020a) Evaluating differences in growth, photosynthetic efficiency, and transcriptome of Asterarcys sp. SCS-1881 under autotrophic, mixotrophic, and heterotrophic culturing conditions. Algal Res. 45: 101753 https://doi.org/10.1016/j.algal.2019.101753 Li Y., Cai X., Gu W., Wang G. (2020b) Transcriptome analysis of carotenoid biosynthesis in Dunaliella salina under red and blue light. J. Oceanol. Limnol. 38: 177–185 Lipinska A. P., Serrano-Serrano M. L., Cormier A., Peters A. F., Kogame K., Cock J. M., Coelho S. M. (2019) Rapid turnover of life-cycle-related genes in the brown algae. Genome Biol. 20: 35 https://doi.org/10.1186/s13059-019-1630-6 Liu C., Wang X., Wang X., Sun C. (2016) Acclimation of Antarctic Chlamydomonas to the sea-ice environment: a transcriptomic analysis. Extremophiles 20: 437–450 Liu Z., Jones A. C., Campbell V., Hambright K. D., Heidelberg K. B., Caron D. A. (2015) Gene expression in the mixotrophic prymnesiophyte, Prymnesium parvum, responds to prey availability. Front. Microbiol. 6: 319 DOI: 10.3389/fmicb.2015.00319 Liu Z., Campbell V., Heidelberg K. B., Caron D. A. (2016) Gene expression characterizes different nutritional strategies among three mixotrophic protists. FEMS Microbiol. Ecol. 92: 2016, fiw106 DOI: 10.1093/femsec/fiw106 Liu Z., Mesrop L. Y., Hu S. K., Caron D. A. (2019a) Transcriptome of Thalassicolla nucleata holobiont reveals details of a radiolarian symbiotic relationship. Front. Mar. Sci. 6: 284 DOI: 10.3389/fmars.2019.00284 Liu J., Sun Z, Mao X., Gerken H., Wang X., Yang W. (2019b) Multiomics analysis reveals a distinct mechanism of oleaginousness in the emerging model alga Chromochloris zofingiensis. Plant J. 98: 1060–1077 Mancipe N. C., McLaughlin E. M., Barney B. M. (2021) Genomic analysis and characterization of Scenedesmus glucoliberatum PABB004: An unconventional sugar-secreting green alga. J. Appl. Microbiol. 00: 1–16 DOI: 10.1111/jam.15311 Manna D., Ehrenkaufer G. M., Lozano-Amado D., Singh U. (2020) Entamoeba stage conversion: Progress and new insights. Curr. Opin. Microbiol. 58: 62–68 Mansfeldt C. B., Richter L. V., Ahner B. A., Cochlan W. P., Richardson R. E. (2016) Use of De Novo transcriptome libraries to characterize a novel oleaginous marine Chlorella species during the accumulation of triacyglycerols. PLOS One 11(2): e0147527 DOI:10.1371/journal.pone.0147527 Mao X., Zhang Y., Wang X., Liu J. (2020a) Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: A multi-omics study. Biotechno. Biofuels 13: 73 https://doi.org/10.1186/s13068-020-01714-y Mao X., Lao Y., Sun H., Li X., Yu J., Chen F. (2020b) Time resolved transcriptome analysis during transitions of sulfur nutritional status provides insight into triacylglycerol (TAG) and astaxanthin accumulation in the green alga Chromochloris zofingiensis. Biotechno. Biofuels 13: 128 https://doi.org/10.1186/s13068-020-01768-y Martins M. J. F., Mota C. F., Pearson G. A. (2013) Sex-biased gene expression in the brown alga Fucus vesiculosus. BMC Genomics 14: 294 http://www.biomedcentral.com/1471-2164/14/294 Massana R., Labarre A., López-Escardó D., Obiol A., Bucchini F., Hackl T., Fischer M. G., Vandepoele K., Tikhonenkov D. V., Husnik F., Keeling P. J. (2021) Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. ISME J. 15: 154–167 Matt G. Y., Umen J. G. (2018) Cell-type transcriptomes of the multicellular green alga Volvox carteri yield insights into the evolutionary origins of germ and somatic differentiation programs. G3 (Bethesda) 8: 531–550 McKie-Krisberg Z. M., Sanders R. W., Gast R. J. (2018) Evaluation of mixotrophy-associated gene expression in two species of polar marine algae. Front. Mar. Sci. 5: 273 DOI:10.3389/ fmars.2018.00273 Mo Y., Peng F., Gao X., Xiao P., Logares R., Jeppesen E., Ren K., Xue Y., Yang J. (2021) Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir. Microbiome 9: 128 DOI.org/10.1186/s40168-021-01079-w Mohamed A. R., Andrade N., Moya A., Chan C. X., Negri A. P., Bourne D. G., Ying H., Ball E. E., Miller D. J. (2020) Dual RNA-sequencing analyses of a coral and its native symbiont during the establishment of symbiosis. Mol. Ecol. 29: 3291–3937 Morse D., Daoust P., Benribague S. (2016) A transcriptome-based perspective of cell cycle regulation in dinoflagellates. Protist 167: 610–621 Mukhtar I., Wu S., Wei S., Chen R., Cheng Y., Liang C., Chen J. (2021) Transcriptome profiling revealed multiple rquA genes in the species of Spirostomum (Protozoa: Ciliophora: Heterotrichea). Front. Microbiol. 11: 574285 DOI: 10.3389/fmicb.2020.574285 Murray S. A., Suggett D. J., Doblin M. A., Kohli G. S., Seymour J. R., Fabris M., Ralph P. J. (2016) Unravelling the functional genetics of dinoflagellates: A review of approaches and opportunities. Perspect. Phycol. 3: 37–52 Naiyer S., Bhattacharya A., Bhattacharya S. (2019) Advances in Entamoeba histolytica biology through transcriptomic analysis. Front. Microbiol. 10: 1921 DOI: 10.3389/fmicb.2019.01921 Nan F., Feng J., Lv J., Liu Q., Xie S. (2018) Transcriptome analysis of the typical freshwater rhodophytes Sheathia arcuata grown under different light intensities. PLoS ONE 13: e0197729 https://doi.org/10.1371/journal. pone.0197729 Nishimura Y., Otagiri M., Yuki M., Shimizu M., Inoue J., Moriya S., Ohkuma M. (2020) Division of functional roles for termite gut protists revealed by single-cell transcriptomes. ISMEJ 14: 2449-2460 Nordin N., Yusof N., Maeda T., Mustapha N. A., Zulkhairi M., Yusoff M. Z. M., Khairuddin R. F. R. (2020) Mechanism of carbon partitioning towards starch and triacylglycerol in Chlorella vulgaris under nitrogen stress through whole-transcriptome analysis. Biomass Bioenergy 138: 105600 https://doi.org/10.1016/j.biombioe.2020.105600 O’Neill E. C., Trick M., Hill L., Rejzek M., Dusi R. G., Hamilton C. J., Zimba P. V. Henrissat B., Field R. A. (2015) The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry. Mol. Bio-Syst. 11: 2808 DOI: 10.1039/c5mb00319a Nowak J. K., Gromadka R., Juszczuk, M., Jerka-Dziadosz M., Maliszewska K., Mucchielli M.-H., Gout J.-F., Arnaiz O., Agier N., Tang T., Aggerbeck L. P., Cohen J., Delacroix H., Sperling L., Herbert C. J., Zagulski M., Bétermier M. (2011) Functional study of genes essential for autogamy and nuclear reorganization in Paramecium. Eukaryot. Cell 10: 363– 372 Orsi W. D., Morard R., Vuillemin A., Eitel M., Wörheide G., Milucka J., Kucera M. (2020) Anaerobic metabolism of Foraminifera thriving below the seafloor. ISMEJ (2020) 14: 2580–2594 https://doi.org/10.1038/s41396-020-0708-1 Ota S., Oshima K., Yamazaki T., Kim S., Yu Z., Yoshihara M., Takeda K., Takeshita T., Hirata A., Bisová K., Zachleder V., Hattori M., Kawano S. (2016) Highly efficient lipid production in the green alga Parachlorella kessleri: draft genome and transcriptome endorsed by whole-cell 3D ultrastructure. Biotechnol. Biofuels 9:13 DOI 10.1186/s13068-016-0424-2 Ouyang L.-L., Chen S.-H., Zhou Z.-G. (2013) Transcriptome analysis reveals unique C4-like photosynthesis and oil body formation in an arachidonic acid-rich microalga Myrmecia incisa Reisigl H4301. BMC Genomics 14: 396 http://www.biomedcentral.com/1471- 2164/14/396 Panchy N., Wu G., Newton L., Tsai C.-H., Chen J., Benning C., Farré E. M., Shiu S.-H. (2014) Prevalence, evolution, and cisregulation of diel transcription in Chlamydomonas reinhardtii. G3 (Bethesda) 4: 2461–2471 Peredo E. L., Cardon Z. G. (2020) Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. Proc. Natl. Acad. Sci. U.S.A. 117: 17438-17445 Phipps S., Delwiche C. F., Bisson M. A. (2021) Salinity-induced changes in gene expression in the streptophyte alga Chara: The critical role of a rare Na+-ATPase. J. Phycol. 57: 1004–1013 Prosser J. I. (2015) Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology. Nat. Rev. Microbiol. 13: 439–446. Proulx S. R., Promislow D. E. L., Phillips P. C. (2005) Network thinking in ecology and evolution. Trends Ecol. Evol. 20: 345–353 Raymond J. A., Remias D. (2019) Ice-binding proteins in a chrysophycean snow alga: Acquistion of an essential gene by horizontal gene transfer. Front. Microbiol. 10: 2697 DOI: 10.3389/fmicb.2019.0269 Remmers I. M., D’Adamo S., Martens D. E., de Vos R. C. H., Mumm R., America A. H. P., Cordewener J. H. G., Bakker L. V., Peters S. A., Wijffels R. H., Lamers P. P. (2018) Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation. Algal Res. 35: 33–49 Ren Z., Wang F., Qu X., Elser J. J., Liu Y., Chu L. (2017) Taxonomic and functional differences between microbial communities in Qinghai Lake and its input streams. Front. Microbiol. 8: 2319 DOI: 10.3389/fmicb.2017.02319 Rippin M., Becker B., Holzinger A. (2017) Enhanced desiccation tolerance in mature cultures of the streptophytic green alga Zygnema circumcarinatum revealed by transcriptomics. Plant Cell Physiol. 58: 2067–2084 Roth M. S., Westcott D. J., Iwai M., Niyogi K. K. (2019) Hexokinase is necessary for glucose- mediated photosynthesis repression and lipid accumulation in a green alga. Commun. Biol. 2: 347 https://doi.org/10.1038/s42003-019-0577-1 Rubin E. T., Cheng S., Montalbano A. L., Menden-Deuer S., Rynearson T. A. (2019) Transcriptomic responses to feeding and starvation in a herbivorous dinoflagellate. Front. Mar. Sci. 6: 246 DOI: 10.3389/fmars.2019.00246 Salavarría E., Paul S., Gil-Kodaka P., Villena G. K. (2018) First global transcriptome analysis of brown algae Macrocystis integrifolia (Phaeophyceae) under marine intertidal conditions. 3 Biotech 8: 185 https://doi.org/10.1007/s13205-018-1204-4 Santoferrara L. F., Guida S., Zhang H., McManus G. B. (2014) De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton. PLoS ONE 9(7): e101418 DOI:10.1371/journal.pone.0101418 Savage A. F., Kolev N. G., Franklin J. B., Vigneron A., Aksoy S., Tschudi C. (2016) Transcriptome Profiling of Trypanosoma brucei development in the tsetse fly vector Glossina morsitans. PLoS ONE 11(12): e0168877 DOI:10.1371/journal.pone.0168877 Saxena A., Lahav T., Holland N., Aggarwal G., Anupama A., Huang Y., Voplin H., Myler P. J., Zilberstein D. (2007) Analysis of the Leishmania donovani transcriptome reveals an ordered progression of transient and permanent changes in gene expression during differentiation. Mol. Biochem. Parasitol. 152: 53–65 Schapp P., Schilde C. (2018) Encystation: The most prevalent and underinvestigated differentiation pathway of eukaryotes. Microbiology 164: 727–739 Shang C., Bi G., Yuan Z., Wang Z., Alam M. A., Xie J. (2016) Discovery of genes for production of biofuels through transcriptome sequencing of Dunaliella parva. Algal Res. 13: 318–326 Shao Z., Zhang P., Lu C., Li S., Chen Z., Wang X., Duan D. (2019) Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis. BMC Genomics 20: 975 https://doi.org/10.1186/s12864-019-6366-x Sirikhachornkit A., Suttangkakul A., Vuttipongchaikij, S., Juntawong P. (2018) De novo transcriptome analysis and gene expression profiling of an oleaginous microalga Scenedesmus acutus TISTR8540 during nitrogen deprivation-induced lipid accumulation. Sci. Rep. 8: 3668 DOI: 10.1038/s41598-018- 22080-8 Song C., Mazzola M., Cheng X., Oetjen J., Alexandrov T., Dlrrestein P., Watrous J., van der Voort M., Raaijmakers J. M. (2015) Molecular and chemical dialogues in bacteria-protozoa interactions. Sci. Rep. 5: 12837 DOI: 10.1038/srep12837 Song H., He M., Wu C., Gu C., Wang C. (2020) Global transcriptomic analysis of an Arctic Chlorella-Arc reveals its eurythermal adaptivity mechanisms. Algal Res. 46: 101792 https://doi.org/10.1016/j.algal.2020.101792 Tan K. W. M., Lin H., Shen H., Lee Y. K. (2016) Nitrogen-induced metabolic changes and molecular determinants of carbon allocation in Dunaliella tertiolecta. Sci. Reports 6: 37235 DOI: 10.1038/srep37235 Van de Poel B., Cooper E. D., Van der Straeten D., Chang C., Delwiche C. F. (2016) Transcriptome profiling of the green alga Spirogyra pratensis (Charophyta) suggests an ancestral role for ethylene in cell wall metabolism, photosynthesis, and abiotic stress responses. Plant Physiol. 172: 533–545 Von Dassow P., Ogata H., Probert I., Wincker P., Da Silva C., Audic S., Claverie J.-M., de Vargas C. (2009) Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. Genome Biol. 10: R114 doi:10.1186/gb-2009-10-10-r114 Wang L., Abu-Doleh A., Plank J., Catalyurek U. V., Firkins J. L., Yu Z. (2019) The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features. BMC Genomics (2019) 20:1008 https://doi.org/10.1186/s12864-019-6382-x Wang N., Qian Z., Luo M., Fan S., Zhang X., Zhang L. (2018) Identification of salt stress responding genes using transcriptome analysis in green alga Chlamydomonas reinhardtii. Int. J. Mol. Sci. 19: 3559 doi:10.3390/ijms19113359 Wang W., Gao X., Ndayishimiye J. C., Lara E., Lahr D. J. G., Qian H., Ren K., Chen H., Yang J. (2021) Population and molecular responses to warming in Netzelia tuberspinifera – An endemic and sensitive protist from East Asia. Sci. Total Environ https://doi.org/10.1016/j.scitotenv.2021.150897 0048-9697 Wilken S., Choi C. J., Worden A. Z. (2020) Contrasting mixotrophic lifestyles reveal different ecological niches in two closely related marine protists. J. Phycol. 56: 52–67 Xing G., Yuan H., Yang J., Li J., Gao Q., Li W., Wang E. (2018) Integrated analyses of transcriptome, proteome and fatty acid profilings of the oleaginous microalga Auxenochlorella protothecoides UTEX 2341 reveal differential reprogramming of fatty acid metabolism in response to low and high temperatures. Algal Res. 33: 16–27 Xiong J., Lu X., Zhou Z., Chang Y., Yuan D., Tian M., Zhou Z., Wang L., Fu C., Orias E., Miao W. (2012) Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using deep RNA sequencing. PLoS ONE 7(2): e30630. DOI:10.1371/journal.pone.0030630 Xu Y., Shen Z., Gentekaki E., Xu J., Yi Z. (2020) Comparative transcriptome analyses during the vegetative cell cycle in the mono-cellular organism Pseudokeronopsis erythrina (Alveolata, Ciliophora). Microorganisms 8: 108 DOI:10.3390/microorganisms8010108 Yang F., Xiang W., Li T., Long L. (2018) Transcriptome analysis for phosphorus starvation- induced lipid accumulation in Scenedesmus sp. Sci. Rep. 8: 16420 DOI:10.1038/s41598-018-34650-x Yeh T.-J., Tseng Y.-F., Chen Y.-C., Hsiao Y., Lee P.-C., Chen T.-J., Chen C.-Y., Kao C.-Y., Chang J.-S., Chen J.-C., Lee T.-M. (2017) Transcriptome and physiological analysis of a lutein-producing alga Desmodesmus sp. reveals the molecular mechanisms for high lutein productivity. Algal Res. 21: 103–119 Yoshida Y., Tomiyama T., Maruta T., Tomita M., Ishikawa T., Arakawa K. (2016) De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions. BMC Genom. 17: 182 DOI: 10.1186/s12864-016-2540-6 Zhang Z., Qu C., Yao R., Nie Y., Xu C., Miao J., Zhong B. (2019) The parallel molecular adaptations to the Antarctic cold environment in two psychrophilic green algae. Genome Biol. Evol. 11: 1897–1908 Zhang Z.-H., Chang X., Su D.-Y., Yao R., Liu X.-D., Zhu H., Liu G.-X., Zhong G.-J. (2020) Comprehensive transcriptome analyses of two Oocystis algae provide insights into the adaptation to Qinghai-Tibet Plateau. J. Syst. Evol. 00: 1–11 DOI: 10.1111/jse.12589 Zhao Y., Hou Y., Chai W., Liu Z., Wang X. , He C., Hu Z., Chen S., Wang W., Chen F. (2020) Transcriptome analysis of Haematococcus pluvialis of multiple defensive systems against nitrogen starvation. Enzyme Microb. Technol. 134: 109487 https://doi.org/10.1016/j.enzmictec.2019.109487 Zones J. M., Blaby I. K., Merchant S. S., Umen J. G. (2015) Highresolution profiling of a synchronized diurnal transcriptome from Chlamydomonas reinhardtii reveals a continuous cell and metabolic differentiation. Plant Cell 27: 2743–2769 Zou S., Zhang Q., Gong J. (2020) Comparative transcriptomics reveals distinct gene expressions of a model ciliated protozoan feeding on bacteria-free medium, digestible, and digestion resistant bacteria. Microorganisms 8: 559 DOI:10.3390/microorganisms8040559