Table 1.
List of microalgae and diatoms with complete or near to complete genome, and the overview of reported omics studies.
| Organism (strain used for genome sequencing) | Genome size (Mb) | Conditions or aim of omics studies | Focus | Accession numbers and references | ||
|---|---|---|---|---|---|---|
| Transcriptomic studies | Proteomic studies | Metabolomic studies/ metabolic models | ||||
|
Auxenochlorella protothecoides (0710) |
22.92 | Response to temperature and phosphate stress; trophic growth conditions; oil accumulation | Response to temperature, nitrogen and phosphorus starvation, ionizing radiation; trophic growth conditions, oil accumulation, | Response to temperature and, phosphate and nitrogen starvation, copper stress; oil accumulation, glycome profiling, trophic growth conditions / Genome scale and core metabolic model | Biofuel | PRJNA428835, PRJNA484804 (Li et al., 2013, 2014b; Gao et al., 2014a; Sibi et al., 2014; Wu et al., 2015; Park and Choi, 2018; Park et al., 2018; Vogler et al., 2018; Xing et al., 2018) |
|
Bathycoccus prasinos (RCC 1105) |
15.07 | Normal growth conditions | - | - | Comparative analysis | PRJNA231566, https://www.imicrobe.us/#/projects/104 |
|
Bigelowiella natans (CCMP2755) |
91.41 | High light stress and small RNA profiling | Profiling of proteins targeted to plastid and peri-plastid space | - | Model Organism | GSE124831, GSE115762 (Hopkins et al., 2012) |
|
Botryococcus braunii (Showa) |
184.32 | Response to nitrogen deprivation, high salt, cobalt enrichment, NaHCO3, salicylic acid, methyl jasmonate, and acetic acid | - | Response to different nutrients, growth phases; tetraterpenoid and hydrocarbons analysis / Genome scale metabolic model | Hydrocarbons and biofuels | FY358876, GES71296, SRP161189, GSE96585 (Molnar et al., 2012; Cornejo-Corona et al., 2016; Thapa et al., 2016; Blifernez-Klassen et al., 2018) |
|
Chlamydomonas debaryana (NIES-2212) |
120.36 | - | - | Oxylipin analysis, lipid profiling in response to different light and CO2 levels | de los Reyes et al., 2014; Toyoshima and Sato, 2015, 2018; Yoshitomi et al., 2019 | |
|
Chlamydomonas reinhardtii (CC-503 cw92 mt+) |
120.4 | Response to nutrient starvation, oxidative and heat stress, high light intensity, diurnal cycle; ciliogenesis; lipid accumulation | Response to nitrogen and sulfur starvation; exposure to high salinity, high CO2, dark and anoxic conditions; lipid mutant, lipid droplet proteins | Response to nitrogen starvation, dark and anoxic conditions / Genome scale and core metabolic model | Model organism | GSE17970, PRJNA379963 (May et al., 2009; Chen et al., 2010; Baba et al., 2011; Nguyen et al., 2011; Longworth et al., 2012; Mastrobuoni et al., 2012; Choi et al., 2013; Chaiboonchoe et al., 2014; Wase et al., 2014; Sithtisarn et al., 2017; Salguero et al., 2019) |
|
Chlorella pyrenoidosa (FACHB-9) |
56.99 | Response to CO2 deprivation, bisphenol A, salt stress, high light stress, glucose starvation and hydroxyl radical; trophic growth conditions | Dried biomass, exposure to inhibitor of mitochondrial respiratory electron transport | Lipid profiling under copper stress and different nitrate levels / Core metabolic model | Biofuels | SRX399080, GSE40028, GSE69816, PRJNA292642, PRJNA526277 (Yang et al., 2000; Sibi et al., 2014; Liu et al., 2018b; Wan et al., 2018; Zhang et al., 2018; Duan et al., 2019) |
|
Chlorella sorokiniana (1230) |
58.53 | Response to nitrogen deprivation, different pH, and high CO2 | Response to inoculum sizes, light intensity and glucose concentrations, nitrogen starvation; bioactive peptide analysis | Response to high-density cultivation and UV radiation; fatty acid profiling | Biofuels | GAPD00000000, GSE98781, GCUV00000000 (Lu et al., 2013; Ma et al., 2013; Rosenberg et al., 2014; Li et al., 2015a; Chen et al., 2017; Kumar et al., 2018; Tejano et al., 2019) |
| Chlorella variabilis (NC64A) | 46.16 | Response to early phase of Chlorella virus-1 infection | - | Nitrogen deprivation and long-chain alkenes/Genome scale metabolic model | Biofuels | SRP026413 (Juneja et al., 2016; Sorigue et al., 2016) |
|
Chlorella vulgaris (NJ-7) |
39.08 | Response to nitrogen starvation and salt stress | Response to nitrogen depletion and repletion, heterotrophic and Na induced lipid accumulation, S-nitrosylated proteome in nitrogen deplete and replete condition | Lipid profiling under copper stress, effect of graphene oxide nanomaterial, N-glycan profiling / Core metabolic model | Biofuels | LDKB00000000 (Guarnieri et al., 2011, 2013; Sibi et al., 2014; Li et al., 2015b; Ouyang et al., 2015; Henard et al., 2017; Zuñiga et al., 2018; Mocsai et al., 2019) |
|
Chloroidium sp. (CF) |
54.31 | - | Normal growth conditions / Genome scale metabolic model | Ecological importance | Nelson et al., 2017, 2019 | |
|
Chromochloris zofingiensis (SAG 211-14) |
58 | Response to nitrogen deprivation, high light; heterotrophic conditions, different growth conditions | Lipid droplets analysis | Lipid and carotenoid profiling in response to glucose | Carotenoids and fatty acids | SRP067324, GSE92515 (Wang et al., 2019c; Zhang et al., 2019) |
|
Coccomyxa sp. (LA000219) |
48.54 | Response to arsenic treatment | - | Response to arsenic treatment | Model organism and biofuels | Koechler et al., 2016 |
|
Coccomyxa subellipsoidea (C-169) |
48.83 | Response to CO2 supplementation; miRNA profiling | - | Response to nitric oxide, cadmium stress, carbon source, nitrogen starvation, phytohormones | Biofuels | GSE76638 PRJNA428141 (Kováčik et al., 2015; Allen et al., 2017; Liu et al., 2018a; Wang et al., 2019e) |
|
Cyanidioschyzon merolae (10D) |
16.55 | Response to diurnal cycle, different CO2 level, blue and red light, UV irradiance | Response to low temperature acclimatization; photosystem II proteins | Response to different CO2 level, diurnal cycle; hydrocarbon and lipid profiling in response to cyanobacterial Acyl-ACP Reductase overexpression | Model organism | GSE37673, GSE83828, GSE100372 (Krupnik et al., 2013; Rademacher et al., 2016; Nikolova et al., 2017; Miyagishima et al., 2019) |
|
Dunaliella salina (CCAP 19/18) |
343.7 | Response to osmotic and oxidative stress, nitrogen depletion, salinity, high light; different growth phases | Response to arsenate, high salinity, high light and high bicarbonate ion level; flagella composition | Response to nitrogen starvation | Halophile, Biofuels, β-carotene and glycerol production | Katz et al., 2007; Jia et al., 2009, 2016; Gu et al., 2014; Ge et al., 2016; Lv et al., 2016; Zhao et al., 2016; Wei et al., 2017b; Wang et al., 2019d |
|
Emiliana huxleyi (CCMP1516) |
167.68 | Response to nitrogen, sulfate and phosphorus starvation, calcium concentrations, elevated temperature and CO2 | Response to different calcium concentration | Response to host-virus (E. huxleyi virus) interaction, phosphorus and nitrogen starvation; lipidomic | Coccolithophore | GSE24341, E-MTAB-2274, SRP017794, SRX756940 (Benner et al., 2013; Rokitta et al., 2014; Hunter et al., 2015; McKew et al., 2015; Wördenweber et al., 2018) |
|
Fistulifera solaris
(JPCC DA0580) |
49.74 | Response of nutrient depleted and replete conditions on lipid accumulation and its degradation | Lipid droplet proteins | - | Biofuels | DRA002404 (Nonoyama et al., 2019) |
|
Fragilariopsis cylindrus (CCMP1102) |
80.54 | Response to temperature, high CO2, prolonged darkness, and nitrogen and iron limitation; small RNA profiling | Response to temperature, salinity stress, prolonged darkness, high CO2, iron starvation | Response to different growth phases | Psychrophile | E-MTAB-5024, GSE57987 (Lyon et al., 2011; Boroujerdi et al., 2012; Kennedy et al., 2019) |
|
Galdieria sulphuraria (074W) |
13.71 | Response to cold acclimation | Photosystem-II analysis | - | Extremophile | PRJNA487158, GSE89169 (Thangaraj et al., 2010) |
|
Guillardia theta (CCMP2712) |
87.15 | Small RNA profiling under light and dark conditions, mRNA splicing analysis | Response to different light intensities | - | Eukaryote endosymbiosis | GSE124831, SRR747855 (Kieselbach et al., 2018) |
|
Haematococcus pluvialis (SAG 192.80) |
365.78 | Response to high light, salinity, iron, acetate, salicylic acid and jasmonic acid, nitrogen depletion and repletion, photooxidative stress; distinct growth phases | Cell wall protein, astaxanthin accumulation, response to high light stress, salicylic acid, and jasmonic acid | Lipid analysis, pigments and protein profiling, live single-cell analysis | Carotenoids | Wang et al., 2004; Tran et al., 2009; Peled et al., 2011; Gu et al., 2014; Recht et al., 2014; Su et al., 2014; Gao et al., 2016; Baumeister et al., 2019; Luo et al., 2019 |
|
Helicosporidium sp. (ATCC 50920) |
12.37 | Transition from free-living organism to obligate intracellular parasite | - | - | Parasite | Pombert et al., 2014 |
|
Klebsormidium nitens (NIES-2285) |
104.21 | Response to auxin treatment and cold stress | - | Response to cold stress | Tolerance to UV and harsh conditions | PRJDB4958, PRJNA500592 (Nagao et al., 2008) |
| Micromonas commoda (RCC299) | 21.11 | Response to different light regimes and ultra-violet light stress | Response to chronic phosphate limitation and subsequent relief, high light and UV-radiation | - | Marine phytoplankton | Cuvelier et al., 2017; Guo et al., 2018 |
|
Micromonas pusilla (CCMP1545) |
21.96 | Response to phycodnavirus MpV-SP1 infection, phosphate deplete and replete, day-night cycle | Phosphate deplete and replete condition, day-night cycle | Response to phosphate deplete and replete condition; different growth phases, | Marine phytoplankton | PRJNA422663 (van Baren et al., 2016; Waltman et al., 2016; Kujawinski et al., 2017) |
|
Micromonas sp. (ASP10-01a) |
19.58 | Normal growth conditions | - | - | Marine phytoplankton | van Baren et al., 2016 |
|
Monoraphidium neglectum
(SAG 48.87) |
69.71 | Nitrogen deprivation | - | - | Biofuels | PRJNA221625 (Jaeger et al., 2017) |
|
Nannochloropsis gaditana (CCMP1894) |
30.86 | Response to light intensity regimes and nitrogen replete and deplete condition | Fresh and atomized biomass | Response to light intensity regimes and nitrogen deprivation / Genome scale metabolic model | Biofuels | Radakovits et al., 2012; Sorigue et al., 2016; Ajjawi et al., 2017; Shah et al., 2017; Fernandez-Acero et al., 2019; Patelou et al., 2020 |
|
Nannochloropsis limnetica (CCMP505) |
33.51 | - | - | Nitrogen deprivation | Biofuels | Sorigue et al., 2016 |
|
Nannochloropsis oceanica (LAMB2011) |
29.26 | Response to different CO2 levels, phosphorus and nitrogen limitation, light and dark cycle, fresh water acclimation; transition from quiescence to autotrophy | Response to long-term nitrogen starvation, low CO2; single-cell-level phenotypic heterogeneity | Response to osmotic downshift and nitrogen depletion | Biofuels | Dong et al., 2013; Pal et al., 2013; Sorigue et al., 2016; Poliner et al., 2018; Chen et al., 2019; Wei et al., 2019 |
|
Nannochloropsis oculate (CCMP525) |
26.27 | - | Nitrogen deprivation, cadmium stress | Nitrogen deprivation | Lipids and protein content | Kim et al., 2005; Sorigue et al., 2016; Tran et al., 2016 |
|
Ostreococcus lucimarinus (CCE9901) |
13.2 | - | - | Genome scale metabolic model | Small genome | Krumholz et al., 2012 |
|
Ostreococcus tauri (RCC4221) |
13.03 | Response to OtV5 virus infection, light and dark cycle, iron limitation, and high light; life cycle stages | Phosphoproteome in response to casein kinase 2, light dark cycle | Glycerolipid profiling under nutrient deprived condition, diurnal variations, nitrogen deprivation / Genome Scale metabolic model | Small genome | Krumholz et al., 2012; Martin et al., 2012; Hindle et al., 2014; Le Bihan et al., 2015; Lelandais et al., 2016; Sorigue et al., 2016; Degraeve-Guilbault et al., 2017; Hirth et al., 2017 |
|
Parachlorella kessleri (NIES-2152) |
59.18 | Response to salt stress and sulfur deplete and replete | Salt stress | Nitrogen, sulfur and phosphorus deprivation | Ota et al., 2016a,b; Shaikh et al., 2019; You et al., 2019 | |
|
Phaeodactylum tricornutum (CCAP 1055/1) |
27.45 | Response to nitrogen, iron, carbon and phosphorus deprivation, cadmium stress, mixotrophic growth, grazing stress, different light intensities, and regimes, salicylic acid; non-coding microRNA | Response to nitrogen limitation, oxidative and dark stress; phosphoproteomics under high light, nitrogen, and iron deficiency | Response to blue and red light, nitrogen and phosphorus deprivation; glycerolipid profile; mixotrophic growth / Genome scale and core metabolic model | Model organism | PRJEB11970, SRX648639 (Chen et al., 2014; Ge et al., 2014; Jungandreas et al., 2014; Rosenwasser et al., 2014; Yang et al., 2014; Abida et al., 2015; Alipanah et al., 2015; Feng et al., 2015; Bai et al., 2016; Longworth et al., 2016; Sorigue et al., 2016; Yoneda et al., 2016; Villanova et al., 2017; Remmers et al., 2018; Smith et al., 2019) |
|
Picochlorum sp. (SENEW3 / DOE 101) |
13.39 / 15.25 | Response to salinity stress and high temperature | - | - | Biofuels | PRJNA245752, PRJNA389600 |
|
Scenedesmus sp. (ARA3, ARA) |
93.24 | Response to phosphorus and nitrogen starvation, lipid accumulation | Response to salinity stress; lipid accumulation | Response to salinity and arsenic stress; lipid accumulation | Biofuels | PRJNA428298 (Chu et al., 2011; Arora et al., 2018, 2019; Wang et al., 2019b) |
|
Scenedesmus obliquus (UTEX393) |
107.72 | Response to diurnal changes and nC60; wild type and starch less mutant comparison | Thylakoid membrane proteome, toxicity of silver nanoclusters | Response to nC60 and silver nanoparticles; different photoperiod and growth phases | Lipid and biomass | E-MTAB-7009 (Kantzilakis et al., 2007; Du et al., 2017; Zhang et al., 2017; Vendruscolo et al., 2019; Wang et al., 2019a) |
|
Symbiodinium minutum (Mf 1.05b.01) |
609.48 | Diurnal cycle, cultured, and freshly isolated cells | - | Response to acidification | Coral symbiont | PRJNA544863 (Jiang and Lu, 2019) |
|
Symbiodinium microadriaticum (CCMP2467) |
808.2 | Response to different temperature, dark, and salinity stress; normal growth conditions, miRNA profiling | - | Response to environmental variation | Coral symbiont | GSE47373, GSE47372 (Klueter et al., 2015; Aranda et al., 2016) |
|
Tetraselmis striata (LANL1001) |
227.95 | Normal growth | - | - | PRJNA231566, https://www.imicrobe.us/#/projects/104 | |
|
Thalassiosira oceanica (CCMP1005) |
92.18 | Response to iron and copper | Response to iron and copper; extracellular superoxide production | - | Model organism | PRJNA382002, SRA045825 (Lommer et al., 2012; Diaz et al., 2019) |
|
Thalassiosira pseudonana (CCMP1335) |
32.44 | Response to nitrogen and phosphorus deprivation, salinity, light intensity, triphenyltin chloride, silicon, CO2 levels, source of light, and nitrogen | Response to nitrogen and phosphorus starvation, light intensity, salinity, triphenyltin chloride, CO2 levels, silicon, micronutrients deficiency, benzo(a)pyrene, K. brevis allelopathy; composition of nano- and micropatterned biosilica cell wall, mitochondrial and plastid proteome | Response to phosphate deplete and replete condition, cobalamin scarcity; K. brevis allelopathy | Model organism | Carvalho and Lettieri, 2011; Dyhrman et al., 2012; Du et al., 2014; Kettles et al., 2014; Kustka et al., 2014; Luo et al., 2014; Poulson-Ellestad et al., 2014; Yi et al., 2014; Jian et al., 2017; Kujawinski et al., 2017; Chen et al., 2018; Heal et al., 2019; Schober et al., 2019 |
|
Trebouxia gelatinosa (LA000220) |
61.73 | Response to dehydration and subsequent rehydration | - | - | Colonization through symbiosis | PRJNA213702 |
|
Volvox carteri f. magariensis (Eve) |
137.68 | Response to low dose of UV-B radiation; somatic and reproductive cells | - | - | Multicellular alga, model organism | E-MTAB-5691 and GSE104835 |
|
Yamagishiella unicocca (NIES-3982) |
134.24 | Normal growth condition | - | - | Multicellular alga, model organism | PRJNA532307 |