BUSCADOR RECOLECTA

Environmental/experimental conditions: Arabidopsis (A. thaliana) WT, ecotype Columbia-0, T-DNA insertion mutants, and transgenic lines (Supplementary Table S4) were routinely grown on soil in growth chambers under long-day (LD) (16 h light/8 h darkness) or SD (8 h light/16 h darkness) photoperiod at 22 and 20 °C during light and dark periods, respectively, and a light intensity of 125 µE m−2 s−1 unless otherwise stated. For HL conditions, 6-wk-old SD grown plants were transferred to continuous HL (930 µE m−2 s−1) for 7 d. T-DNA insertion mutants 2cpab (Ojeda et al. 2018), Δ2cp (Pulido et al. 2010), ntrc (Serrato et al. 2004), prxQ (Lamkemeyer et al. 2006), prxIIE (Romero-Puertas et al. 2007), and fad7 and fad8 (Román et al. 2015) were previously reported. Transgenic lines overexpressing 2CPA (2CPA-OE), NTRC (NTRC-OE) or FAD8 (WT/FAD8–YFP–HA) under the control of the CaMV 35S promoter in the Col-0 background, were previously described by Pérez-Ruiz et al. (2017), Ojeda et al. (2018), and Román et al. (2015), respectively. Transgenic lines 2cpab/2CPA-OE, 2cpab/2CPA-CP-S-OE, 2cpab/FAD8–YFP–HA, WT/FAD8–CFP–HA, and 2cpab/FAD8–CFP–HA were generated in this study as described below. Escherichia coli and Agrobacterium tumefaciens (strain GV3101) were grown in liquid Miller nutrient at 37 and 28 °C, respectively, with the appropriate antibiotics., People involved with sample collection, processing, analysis and/or submission, please specify using CREDIT roles https://credit.niso.org/: M.L.H., F.J.C., and J.M.P.-R. conceived and designed the study. M.L.H. performed lipid analysis, Native-PAGE gel electrophoresis and immunoblotting, and confocal microscopy. J.J.-L. conducted the Co-IP assay. M.L.H and J.J.-L. performed SDS–PAGE gel electrophoresis and immunoblotting. J.M.P.-R. constructed transgenic lines, analyzed genes expression levels by RT-qPCR, and conducted thiol labeling assay., Vector construction and generation of transgenic plants For the generation of 2cpab/2CPA-OE and 2cpab/2CPA-CP-S-OE transgenic lines, cDNA was synthesized with the Maxima first strand cDNA synthesis kit (Thermo Scientific) from total RNA isolated from WT Arabidopsis leaves using Trizol reagent (Invitrogen). The cDNA sequence coding for 2-Cys PRX A, including the stop codon, was amplified with iProof High-Fidelity DNA Polymerase (Bio-Rad) using specific oligonucleotides (Supplementary Table S5) that added attB recombination sites at the 5′ and 3′ ends, respectively. The PCR product was cloned in the Gateway compatible vector pDONR221 (Invitrogen) and confirmed by sequencing. The 2CPA-CP-S mutant version, in which the peroxidatic Cys (CP) of 2-Cys Prx A was replaced by Ser (C119S: codon change TGC > AGC), was generated by site-directed mutagenesis as reported in (Pérez-Ruiz et al. 2006), using the pDONR221/2CPA plasmid and specific oligonucleotides (Supplementary Table S5). Plasmids pDONR221/2CPA and pDONR221/2CPA-CP-S were then subcloned into the binary vector pEARLEYGATE100 using LR clonase (Invitrogen) according to the manufacturer´s instructions. Constructed vectors were introduced into A. tumefaciens (GV3101) and transformed into the 2cpab mutant by the floral dipping method (Clough and Bent 1998). For the generation of 2cpab/FAD8–YFP–HA transgenic line, the WT/FAD8–YFP–HA line (Román et al. 2015), which harbors the BASTA resistance, was manually crossed with the 2cpab double mutant. Plants resulting from this cross were checked for heterozygosity of the T-DNA insertions in the 2-Cys PRX A and 2-Cys PRX B genes and self-pollinized. The 2cpab/FAD8–YFP–HA line was identified in the progeny based on the BASTA resistance and by PCR analysis of genomic DNA with oligonucleotides listed in Supplementary Table S5. For the generation of WT/FAD8–CFP–HA and 2cpab/FAD8–CFP–HA transgenic lines, the genomic fragment of FAD8 excluding the stop codon (2,012 bp) was amplified with iProof High-Fidelity DNA Polymerase (Bio-Rad) using specific oligonucleotides (Supplementary Table S5) that added attB recombination sites at the 5′ and 3′ ends, respectively. The PCR product was cloned in the Gateway compatible vector pDONR221 (Invitrogen) and confirmed by sequencing. Resulting plasmid pDONR221/FAD8 was then subcloned, as indicated above, into the binary vector pEARLEYGATE102, which add CFP and HA C-terminal tags. Constructed vector was introduced into A. tumefaciens (GV3101) and transformed into the WT and 2cpab genetic backgrounds as described above. Protein extraction, western blot analysis and alkylation assays Plant tissues, frozen in liquid nitrogen, were ground to a fine powder using mortar and pestle. For total protein analysis, extraction buffer A (50 mM Tris–HCl, pH 8.0, 0.15 M NaCl, 0.5% (v/v) Nonidet P-40) was immediately added, mixed on a vortex, and centrifuged at 16,100 × g at 4 °C for 20 min. For FAD8–YFP–HA protein analysis, powdered samples were resuspended in 50 mM Tris–HCl, pH 7.8, 2.5% (vol/vol) glycerol, 4 M urea, and 2% SDS. For the separation of soluble and membrane protein fractions, the powder was resuspended in buffer B (25 mM HEPES–KOH, pH 7.4, 10 mM MgCl2, 0.2 mM phenylmethanesulfonyl fluoride, 5 mM aminocaproic acid) and filtered through a layer of Miracloth paper (Calbiochem, Darmstadt, Germany). After centrifugation, 6,000 × g at 4 °C for 5 min, the supernatant was collected as the soluble fraction and the pellet containing the membrane proteins was solubilized in buffer C (50 mM Tris–HCl, pH 8, 0.15 M NaCl, 1% (w/v) digitonin, 1% (w/v) n-dodecyl-β-D-maltoside), incubated on ice for 10 min and centrifuged at 13,500 × g at 4 °C for 10 min. After centrifugation, supernatant was collected as the membrane fraction. Protein samples were quantified using the Bradford reagent (Bio-Rad). Protein extracts were subjected to SDS–PAGE under reducing (NTRC, 2-Cys Prxs, FAD8-YFP-HA, CHL27) or nonreducing (2-Cys Prxs) conditions using acrylamide gel concentration of 12%. For 1D-NATIVE-PAGE, membrane proteins were separated by nondenaturing electrophoresis (3% to 12% or 5% to 12% acrylamide gradient) at 4 °C and at 30 V overnight. For 2D-SDS–PAGE, resolving proteins by native electrophoresis was followed by separation in a second dimension with denaturing SDS–PAGE (12% acrylamide). Proteins resolved under denaturing or nondenaturing conditions, as indicated, were transferred to nitrocellulose membranes and probed with specific antibodies for NTRC (Serrato et al. 2004), 2-Cys Prxs (Pérez-Ruiz et al. 2006), HA, and CHL27 (Agrisera). Thiol labeling assay by the alkylating agent MM(PEG)24 was performed as previously described (Pérez-Ruiz et al. 2017). Lipid analysis Total lipids were extracted from Arabidopsis leaves using the chloroform/methanol method described by Li-Beisson et al. (2013), and lipids separation was carried out by thin-layer chromatography as described (Hernández et al. 2008). Fatty acid methyl esters of total lipids or individual lipid classes were produced by acid-catalyzed transmethylation (Garcés and Mancha 1993) and analyzed by gas chromatography using a GC-MS-QP2010 Plus (Shimadzu, Kyoto, Japan) fitted with a Suprawax 280 capillary column (10 m length, 0.1 mm i.d., and 0.1 µm film thickness) and one quadrupole mass detector. Helium was used as the carrier gas at a flow rate of 16.3 mL/min. Ion source was held at a temperature of 200 °C, and an interphase temperature of 280 °C. Heptadecanoic acid was used as internal standard for lipid content calculations. Lipidomic analyses were performed by the Analytical Laboratory of the Kansas Lipidomics Research Center (KLRC) at Kansas State University. The profiles of galactolipid molecular species were measured by an automated electrospray ionization–tandem mass spectrometry methods described by Welti et al. (2002). RT-qPCR Quantitative PCR (qPCR) was performed using cDNA synthesized as stated above in a IQ2 real-time PCR detection system (Bio-Rad) as previously reported (Pérez-Ruiz et al. 2017). Oligonucleotides used for qPCR analyses are listed in Supplementary Table S5. Expression levels were normalized using ACTIN2 and UBQ10 as reference genes. Confocal microscopy analysis Subcellular localization of FAD8 was analyzed by confocal laser scanning microscopy (FLUOVIEW FV3000, Olympus) of leaves dissected from WT/FAD8–YFP–HA and 2cpab/FAD8–YFP–HA transgenic plants, expressing the corresponding FAD8–YFP–HA fusion protein. Images were acquired with a UPlanXApo 40x/1.4 NA oil immersion objective. Samples were excited with 488 nm laser at 1% of intensity, and fluorescence emission was collected across windows of 520 to 570 nm on high-sensitivity spectral detectors at 450 V, 1× of gain and 4% of offset for YFP and 650 to 750 nm and at 360–430 V, 1× of gain and 4% of offset for chlorophyll autofluorescence. Images were analyzed using Olympus FV31S-SW (Olympus Corporation) and ImageJ software (National Institute of Health, USA). Immunoprecipitation Rosette leaves from WT/FAD8–YFP–HA, WT/FAD8–CFP–HA#3, and WT plants, used as a negative control, were fixed with 1% (v/v) formaldehyde by vacuum infiltration for 35 min. Cross-linking reaction was stopped by adding 300 mM glycine followed by three washes with Milli-Q water. Membrane protein fractions (∼840 µg), obtained as described above, were incubated with 30 µL HA magnetic beads (Invitrogen) at 4 °C for 1.5 h on a rotating wheel. The beads were washed three times with 50 mM Tris–HCl, pH 7.5, 150 mM NaCl, 5% (v/v) glycerol, and 0.05% (v/v) Nonidet P40 and then two times with 50 mM Tris–HCl, pH 7.5, 150 mM NaCl and 5% (v/v) glycerol. Proteins were eluted from the beads by 10 min boiling in 100 µL SDS–PAGE loading buffer., Grant PID2020-115156 GB-I00 funded by Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación/10.13039/501100011033., Peer reviewed

Three human teeth from the Middle Palaeolithic archaeological levels of Arbreda Cave (Serinyà, Catalonia, NE Iberian Peninsula). The teeth, two molars (one right dm2 and one right M2) from Level N (older than 120 kyr) and one P3 from Level J (dated between 71 and 44 kyr), belong to a minimum number of two individuals: one adult and one juvenile. The premolar from Mousterian Level J, the best preserved of the three teeth, exhibits characteristics similar to those from our comparative sample of Homo neanderthalensis, such as the crown measurements, EDJ traits, enamel thickness and volume of the pulp cavity. In the two teeth from Level N, although their high degree of dental wear and poor state of preservation preclude definitive taxonomic designations, the crown dimensions and some tissue proportions point to probable assignation to Homo neanderthalensis., CLT009/18/00092 2017SGR-1688 PID2019-103987GB-C32 MICINN PID2021-122355NB-C32 2021 SGR 01239 MSCa Neander-TALe, project number 89571 University of Bordeaux's IdEx "Investments for the Future" program / GPR Human Past EVODIBIO and EURAPAL teams from PACEA-UMR5199 ANR AERC005, Peer reviewed

There will not be restrictions to use the generated data after its publication, but external users will be asked to cite the source and/or the papers properly, and the redistribution of the data must be authorized by the researcher/supervisor. The identity of the person accessing the data will be ascertained with the following questionnaire, there won't be a need for a data access committee., Raw data obtained with nLGAD silicon detectors fabricated at IMB-CNM-CSIC for the paper: "nLGAD gain response to low-penetrating particles”, Spanish Ministry of Science, Innovation and Universities (MICIU/AEI/10.13039/501100011033/) and by the European Union’s ERDF program “A way of making Europe”. Grant references: CEX2023-001397-M, PID2020-113705RB-C32, PID2021-124660OB-C22, PDC2021-121718-C32 and PDC2023-145925-C32 European Union’s Horizon 2020 Research and Innovation. Grant Agreement No. 101004761 (AIDAInnova) NextGenerationEU, Spain (PRTR-C17.I1). CNA is also partially funded by the ASTRO21/1.1/1 (European Union- NextGenerationEU, the Ministry of Science, Innovation and Universities, Recovery Plan, Transformation and Resilience, Spain, the Department of University, Research and Innovation of the Junta de Andalucia and the University of Sevilla)., Peer reviewed

P. Martini et al. -- Supplementary material to DESI's publication "Validation of the DESI 2024 Lyman Alpha Forest BAL Masking Strategy" to comply with the data management plan., Peer reviewed

Samples were taen in the field and processed in the laboratory following details described in the publication, The MCIN/AEI/10.13039/501100011033 and the “European Unión NextGenerationEU/PRTR supported the grant TED2021-129169B-I00. This study was also financed by the Instituto de Estudios Riojanos (IER, Government of La Rioja, ref. Resolución 17/2019) and the Consejería de Agricultura, Ganaderia, Mundo Rural, Territiorio y Población (Government of La Rioja, ref. P.R.-06-22). The MCIN/AEI/10.13039/501100011033 and the “European Unión NextGenerationEU/PRTR supported RBP Juan de la Cierva contract ref. JDC2022-048978-I, Peer reviewed

File name: Supplementary Data 1 Description: Functional evidences of the suggested SCO-associated signals. File name: Supplementary Data 2 Description: Functional annotation analysis of TAF1B and TJP1 genes. File name: Supplementary Data 3 Description: Polymorphisms with the lowest Pvalues from the transethnic meta-analysis of SCO, focusing on genetic regions encoding members of the TAF1B and TJP1 protein-protein interaction networks. File name: Supplementary Data 4 Description: PheWAS results for rs7873478 in the DMRT1 region. File name: Supplementary Data 5 Description: PheWAS results for rs13206743 in the IL17A region. File name: Supplementary Data 6 Description: PheWAS results for rs34915133 in the HLA-DQA1/HLA-DRB1 region. File name: Supplementary Data 7 Description: PheWAS results for rs10842262 in the SOX5 region. File name: Supplementary Data 8 Description: PheWAS results for rs4492992 in the TJP1 region. File name: Supplementary Data 9 Description: PheWAS results for rs112307255 in the TAF1B region. File name: Supplementary Data 10 Description: Non-MHC previously reported genetic associations with SPGF subtypes at genomewide significance, analyzed for effects on NOA and SCO in the trans-ethnic meta-analysis. File name: Supplementary Data 11 Description: Polymorphisms with the lowest Pvalues in the trans-ethnic meta-analysis across the previously non-MHC reported risk loci for NOA at the genome-wide level of significance. File name: Supplementary Data 12 Description: The source data used to generate the plot located at the top left in supplementary figure 1. File name: Supplementary Data 13 Description: The source data used to generate the plot located at the top right in supplementary figure 1. File name: Supplementary Data 14 Description: The source data used to generate the plot located at the bottom left in supplementary figure 1. File name: Supplementary Data 15 Description: The source data used to generate the plot located at the bottom right in supplementary figure 1., Peer reviewed

File List: Fig. S1 Exposure of Chlamydomonas urium and Chlamydomonas reinhardtii cells to low pH, toxic concentrations of heavy metals or organic carbon. Fig. S2 Growth rate of Chlamydomonas urium and Chlamydomonas reinhardtii cells grown in HSM liquid medium at pH 7 under normal light or high light. Fig. S3 Total chlorophyll levels of Chlamydomonas urium and Chlamydomonas reinhardtii. Fig. S4 Photosynthetic parameters of Chlamydomonas urium and Chlamydomonas reinhardtii cells. Fig. S5 ATG8 proteins from Chlamydomonas urium and Chlamydomonas reinhardtii. Fig. S6 Electron microscopy images of Chlamydomonas urium cells subjected to nitrogen starvation in the presence of ConcA. Fig. S7 Comparative metabolic analysis of Chlamydomonas urium and Chlamydomonas reinhardtii cells grown in HSM medium under normal conditions. Fig. S8 Oxygen production and relative electron transport rate in Chlamydomonas urium and Chlamydomonas reinhardtii in the absence or presence of ConcA. Table S1 List of species used in the study. Table S2 Genes involved in lipid degradation in Chlamydomonas reinhardtii and Chlamydomonas urium. Table S3 Statistical analysis from main figures., Autophagy is a central degradative pathway highly conserved among eukaryotes, includingmicroalgae, which remains unexplored in extremophilic organisms. In this study, we describedand characterized autophagy in the newly identified extremophilic green microalga Chlamy-domonas urium, which was isolated from an acidic environment. The nuclear genome of C. urium was sequenced, assembled and annotated in order toidentify autophagy-related genes. Transmission electron microscopy, immunoblotting, meta-bolomic and photosynthetic analyses were performed to investigate autophagy in this extre-mophilic microalga. The analysis of the C. urium genome revealed the conservation of core autophagy-relatedgenes. We investigated the role of autophagy in C. urium by blocking autophagic flux withthe vacuolar ATPase inhibitor concanamycin A. Our results indicated that inhibition of autop-hagic flux in this microalga resulted in a pronounced accumulation of triacylglycerols and lipiddroplets (LDs). Metabolomic and photosynthetic analyses indicated that C. urium cells withimpaired vacuolar function maintained an active metabolism. Such effects were not observedin the neutrophilic microalga Chlamydomonas reinhardtii. Inhibition of autophagic flux in C. urium uncovered an active recycling of LDs through lipo-phagy, a selective autophagy pathway for lipid turnover. This study provided the metabolicbasis by which extremophilic algae are able to catabolize lipids in the vacuole, This work was supported in part by the Ministerio de Ciencia, Innovación y Universidades (grants PID2021-123500NB-I00 to JLC, PID2019-110080GB-I00 to MEPP and TED2021-130912B-I00 to JLC and MEPP), CSIC (grant 2023AEP102 to MEPP) and Junta de Andalucía (grant P20_00057 to JLC), a Juan de la Cierva postdoctoral contract (FJC2021-048000-I) to MJMP, and a predoctoral contract (PRE2022-102797) to YOG., Peer reviewed

Additional information about the community assembly experiment, Peer reviewed

Derivation of the stationary distribution of abundance for the SLM with a constant rate of migration., Peer reviewed

There will not be restrictions to use the generated data after its publication, but external users will be asked to cite the source and/or the papers properly, and the redistribution of the data must be authorized by the researcher/supervisor. The identity of the person accessing the data will be ascertained with the following questionnaire, there won't be a need for a data access committee, Raw data obtained with nLGAD silicon detectors fabricated at IMB-CNM-CSIC for the paper: "Gain measurements on NLGAD detectors”, Spanish Ministry of Science, Innovation and Universities (MICIU/AEI/10.13039/501100011033/) and by the European Union’s ERDF program “A way of making Europe”. Grant references: RTI2018-094906-B-C22 and PID2020-113705RB-C32. European Union’s Horizon 2020 Research and Innovation. Grant Agreement No. 101004761 (AIDAInnova)., Peer reviewed