{ "metadata": { "name": "AstroGrass Database", "version": "2.1.0", "curator": "Richard Barker (Collaborative Science Environment Inc.)", "primary_study": "NASA OSDR OSD-375 (APEX-06)", "total_genes": 29, "verified_arabidopsis_anchors": 29, "brachypodium_gene_ids": "Orthologs of the Arabidopsis anchor in Ensembl Compara (plants); see data/genotypes/compara_orthologs.csv", "expression_values": "DESeq log2 fold change (ISS / ground) and adjusted p-value from Su et al. (2023) Life 13:626, Supplemental Tables S2-S4 (CC BY 4.0), listed only where Su et al. report the gene as a DEG", "total_studies": 5, "organism": "Brachypodium distachyon", "date_updated": "2026-10-14" }, "studies": [ { "study_id": "OSD-375", "title": "Transcriptional profiling of roots and shoots from Brachypodium distachyon seedlings flown on the ISS", "mission": "SpaceX-14 (launched 2 April 2018); APEX-06", "hardware": "APEX Growth Units in VEGGIE", "organism": "Brachypodium distachyon", "accessions": "Bd21, Bd21-3, Gaz8", "tissues": "Roots, Shoots", "assays": "RNA-Seq (Illumina NovaSeq 6000)", "doi": "10.26030/2x6b-3v89", "reference": "Su et al. (2023) Life 13(3):626, doi:10.3390/life13030626", "category": "Spaceflight (ISS)" }, { "study_id": "OSD-622", "title": "Microgravity effects on leaf morphology, cell structure, carbon metabolism and mRNA expression of dwarf wheat", "mission": "STS-110 to the ISS (PESTO; launched 8 April 2002, returned on STS-111)", "hardware": "Biomass Production System (BPS), PESTO root modules", "organism": "Triticum aestivum", "accessions": "USU Apogee", "tissues": "Leaves (pooled for the microarray)", "assays": "DNA microarray (GenePix)", "doi": "10.26030/m2eg-jx23", "reference": "Stutte et al. (2006) Planta 224:1038-1049, doi:10.1007/s00425-006-0290-4", "category": "Spaceflight (ISS)" }, { "study_id": "GSE97940", "title": "RNA-Sequencing of 2,4-D treated Brachypodium distachyon roots containing NLS", "mission": "Ground study: 2,4-D-induced nodule-like structures (NLS)", "hardware": "Not stated in record", "organism": "Brachypodium distachyon", "accessions": "Not stated in record", "tissues": "Roots with nodule-like structures; untreated roots", "assays": "RNA-Seq (Illumina HiSeq 2500)", "doi": "10.1007/s10142-018-0594-z", "reference": "Thomas et al. (2018) Funct Integr Genomics 18:315-326", "category": "Ground study (auxin treatment)" }, { "study_id": "GSE48040", "title": "A global profiling of gene expression under cold stress in Brachypodium", "mission": "Ground study: cold treatment (4 degC, 24 h)", "hardware": "Not stated in record", "organism": "Brachypodium distachyon", "accessions": "ABR5", "tissues": "Seedlings (12 days old)", "assays": "RNA-Seq (Illumina HiSeq 2000)", "doi": "10.1186/gb-2013-14-8-r92", "reference": "Zhang et al. (2013) Genome Biol 14:R92", "category": "Ground study (cold stress)" }, { "study_id": "PXD000868", "title": "Large-scale phosphoproteome analysis in seedling leaves of Brachypodium distachyon L", "mission": "Ground study: phosphoproteome", "hardware": "Not stated in record", "organism": "Brachypodium distachyon", "accessions": "Not stated in record", "tissues": "Seedling leaves", "assays": "LC-MS/MS phosphoproteomics", "doi": "10.1186/1471-2164-15-375", "reference": "Lv et al. (2014) BMC Genomics 15:375", "category": "Proteomics" } ], "genes": [ { "candidate": "BdPIN1a", "pathway": "Auxin Efflux Carrier", "arabidopsis_gene": "PIN1", "arabidopsis_agi": "AT1G73590", "anchor_status": "verified: UniProt Q9C6B8 (PIN1 At1g73590 F6D5.2)", "brachypodium_orthologs": "BRADI_1g45020v3 BRADI_3g59520v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os02g0743400 Os06g0232300", "wheat_orthologs": "TraesCS6A02G308600 TraesCS6B02G337300 TraesCS6D02G287800 TraesCS7A02G190600 TraesCS7B02G095500 TraesCS7D02G191600", "ortholog_note": "Brachypodium ortholog(s) shared with BdPIN1b", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdPIN1b", "pathway": "Auxin Efflux Carrier", "arabidopsis_gene": "PIN1", "arabidopsis_agi": "AT1G73590", "anchor_status": "verified: UniProt Q9C6B8 (PIN1 At1g73590 F6D5.2)", "brachypodium_orthologs": "BRADI_1g45020v3 BRADI_3g59520v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os02g0743400 Os06g0232300", "wheat_orthologs": "TraesCS6A02G308600 TraesCS6B02G337300 TraesCS6D02G287800 TraesCS7A02G190600 TraesCS7B02G095500 TraesCS7D02G191600", "ortholog_note": "Brachypodium ortholog(s) shared with BdPIN1a", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdPIN2", "pathway": "Auxin Efflux Carrier", "arabidopsis_gene": "PIN2", "arabidopsis_agi": "AT5G57090", "anchor_status": "verified: UniProt Q9LU77 (PIN2 AGR AGR1)", "brachypodium_orthologs": "BRADI_1g31530v3", "brachypodium_homology": "one2one", "rice_orthologs": "Os06g0660200", "wheat_orthologs": "TraesCS7A02G492400 TraesCS7B02G398100 TraesCS7D02G478800", "ortholog_note": "", "su2023_deg_calls": 4, "su2023_degs": "Bd21 root -1.87 (BRADI_2g52640v3, Su et al. best hit); Bd21-3 root -1.32 (BRADI_2g52640v3, Su et al. best hit); Gaz8 root -0.78 (BRADI_1g31530v3, Compara); Gaz8 shoot +2.05 (BRADI_1g31530v3, Compara)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_2g52640v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Bd21", "organ": "root", "deseq_log2fc": -1.86830552565894, "deseq_padj": 0.0015622582004811, "edger_log2fc": -1.8689888483835, "edger_q": 1.2376899709631e-06 }, { "brachypodium_gene_id": "BRADI_2g52640v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Bd21-3", "organ": "root", "deseq_log2fc": -1.31817516483231, "deseq_padj": 0.0041762835120458, "edger_log2fc": -1.31549051217658, "edger_q": 4.58904212043093e-06 }, { "brachypodium_gene_id": "BRADI_1g31530v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_one2one", "accession": "Gaz8", "organ": "root", "deseq_log2fc": -0.776272009806853, "deseq_padj": 7.26659544863632e-08, "edger_log2fc": -0.778278316904178, "edger_q": 0.0002785965292954 }, { "brachypodium_gene_id": "BRADI_1g31530v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_one2one", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": 2.04904595946255, "deseq_padj": 0.0388625271933676, "edger_log2fc": 1.99207383617344, "edger_q": 0.0111868017316578 } ] }, { "candidate": "BdPIN3", "pathway": "Auxin Efflux Carrier", "arabidopsis_gene": "PIN3", "arabidopsis_agi": "AT1G70940", "anchor_status": "verified: UniProt Q9S7Z8 (PIN3 At1g70940 F15H11.14)", "brachypodium_orthologs": "BRADI_2g15610v3 BRADI_2g44987v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os01g0643300 Os05g0576900", "wheat_orthologs": "TraesCS1A02G415400 TraesCS1B02G445400 TraesCS1D02G422900 TraesCS3A02G231500 TraesCS3B02G260700 TraesCS3D02G221900", "ortholog_note": "Brachypodium ortholog(s) shared with BdPIN4, BdPIN7", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdPIN4", "pathway": "Auxin Efflux Carrier", "arabidopsis_gene": "PIN4", "arabidopsis_agi": "AT2G01420", "anchor_status": "verified: UniProt Q8RWZ6 (PIN4 At2g01420 F2I9.4)", "brachypodium_orthologs": "BRADI_2g15610v3 BRADI_2g44987v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os01g0643300 Os05g0576900", "wheat_orthologs": "TraesCS1A02G415400 TraesCS1B02G445400 TraesCS1D02G422900 TraesCS3A02G231500 TraesCS3B02G260700 TraesCS3D02G221900", "ortholog_note": "Brachypodium ortholog(s) shared with BdPIN3, BdPIN7", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdPIN7", "pathway": "Auxin Efflux Carrier", "arabidopsis_gene": "PIN7", "arabidopsis_agi": "AT1G23080", "anchor_status": "verified: UniProt Q940Y5 (PIN7 AEH1 At1g23080)", "brachypodium_orthologs": "BRADI_2g15610v3 BRADI_2g44987v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os01g0643300 Os05g0576900", "wheat_orthologs": "TraesCS1A02G415400 TraesCS1B02G445400 TraesCS1D02G422900 TraesCS3A02G231500 TraesCS3B02G260700 TraesCS3D02G221900", "ortholog_note": "Brachypodium ortholog(s) shared with BdPIN3, BdPIN4", "su2023_deg_calls": 1, "su2023_degs": "Bd21 shoot +2.39 (BRADI_4g26300v3, Su et al. best hit)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_4g26300v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Bd21", "organ": "shoot", "deseq_log2fc": 2.39428573073454, "deseq_padj": 0.0001353792759031, "edger_log2fc": 2.39648731532539, "edger_q": 0.0003054985153619 } ] }, { "candidate": "BdAUX1", "pathway": "Auxin Influx Carrier", "arabidopsis_gene": "AUX1", "arabidopsis_agi": "AT2G38120", "anchor_status": "verified: UniProt Q96247 (AUX1 AUX PIR1)", "brachypodium_orthologs": "BRADI_1g68350v3 BRADI_2g55340v3 BRADI_3g21090v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os01g0856500 Os03g0244600 Os05g0447200 Os10g0147400 Os11g0169200", "wheat_orthologs": "TraesCS1A02G077800 TraesCS1A02G278400 TraesCS1B02G095900 TraesCS1B02G287300 TraesCS1D02G079900 TraesCS1D02G277600 TraesCS3A02G369200 TraesCS3B02G401000 TraesCS3D02G362100 TraesCS4A02G070500 TraesCS4A02G207600 TraesCS4B02G111100 TraesCS4B02G226500 TraesCS4D02G108800 TraesCS4D02G227200", "ortholog_note": "Brachypodium ortholog(s) shared with BdLAX1", "su2023_deg_calls": 2, "su2023_degs": "Gaz8 root -0.60 (BRADI_3g21090v3, Compara); Gaz8 shoot -0.71 (BRADI_3g21090v3, Compara)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_3g21090v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_many2many", "accession": "Gaz8", "organ": "root", "deseq_log2fc": -0.604824263981536, "deseq_padj": 0.0172547967532295, "edger_log2fc": -0.606548144144981, "edger_q": 0.0009456647786443 }, { "brachypodium_gene_id": "BRADI_3g21090v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_many2many", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": -0.712215793367656, "deseq_padj": 0.0301634074832825, "edger_log2fc": -0.738531522820966, "edger_q": 0.0088257470878627 } ] }, { "candidate": "BdLAX1", "pathway": "Auxin Influx Carrier", "arabidopsis_gene": "LAX1", "arabidopsis_agi": "AT5G01240", "anchor_status": "verified: UniProt Q9LFB2 (LAX1 At5g01240 F7J8_220)", "brachypodium_orthologs": "BRADI_1g68350v3 BRADI_2g55340v3 BRADI_3g21090v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os01g0856500 Os03g0244600 Os05g0447200 Os10g0147400 Os11g0169200", "wheat_orthologs": "TraesCS1A02G077800 TraesCS1A02G278400 TraesCS1B02G095900 TraesCS1B02G287300 TraesCS1D02G079900 TraesCS1D02G277600 TraesCS3A02G369200 TraesCS3B02G401000 TraesCS3D02G362100 TraesCS4A02G070500 TraesCS4A02G207600 TraesCS4B02G111100 TraesCS4B02G226500 TraesCS4D02G108800 TraesCS4D02G227200", "ortholog_note": "Brachypodium ortholog(s) shared with BdAUX1", "su2023_deg_calls": 2, "su2023_degs": "Gaz8 root -0.60 (BRADI_3g21090v3, Compara); Gaz8 shoot -0.71 (BRADI_3g21090v3, Compara)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_3g21090v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_many2many", "accession": "Gaz8", "organ": "root", "deseq_log2fc": -0.604824263981536, "deseq_padj": 0.0172547967532295, "edger_log2fc": -0.606548144144981, "edger_q": 0.0009456647786443 }, { "brachypodium_gene_id": "BRADI_3g21090v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_many2many", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": -0.712215793367656, "deseq_padj": 0.0301634074832825, "edger_log2fc": -0.738531522820966, "edger_q": 0.0088257470878627 } ] }, { "candidate": "BdLAX2", "pathway": "Auxin Influx Carrier", "arabidopsis_gene": "LAX2", "arabidopsis_agi": "AT2G21050", "anchor_status": "verified: UniProt Q9S836 (LAX2 At2g21050 F26H11.19)", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 2, "su2023_degs": "Gaz8 root -0.60 (BRADI_3g21090v3, Su et al. best hit); Gaz8 shoot -0.71 (BRADI_3g21090v3, Su et al. best hit)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_3g21090v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Gaz8", "organ": "root", "deseq_log2fc": -0.604824263981536, "deseq_padj": 0.0172547967532295, "edger_log2fc": -0.606548144144981, "edger_q": 0.0009456647786443 }, { "brachypodium_gene_id": "BRADI_3g21090v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": -0.712215793367656, "deseq_padj": 0.0301634074832825, "edger_log2fc": -0.738531522820966, "edger_q": 0.0088257470878627 } ] }, { "candidate": "BdLAX3", "pathway": "Auxin Influx Carrier", "arabidopsis_gene": "LAX3", "arabidopsis_agi": "AT1G77690", "anchor_status": "verified: UniProt Q9CA25 (LAX3 At1g77690 T32E8.2)", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdLAZY1", "pathway": "Gravity Perception/Transduction", "arabidopsis_gene": "LAZY1", "arabidopsis_agi": "AT5G14090", "anchor_status": "verified: UniProt Q5XV40 (LAZY1 LA1 LZY1); corrected on 2026-10-14 from AT5G14660, which is PDF1B/DEF2", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdDRO1", "pathway": "Root Gravitropic Setpoint", "arabidopsis_gene": "DRO1", "arabidopsis_agi": "AT1G72490", "anchor_status": "verified: UniProt Q5XVG3 (LAZY4 DRO1 LZY3)", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 1, "su2023_degs": "Bd21 root +2.54 (BRADI_4g31290v3, Su et al. best hit)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_4g31290v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Bd21", "organ": "root", "deseq_log2fc": 2.54315132442596, "deseq_padj": 0.0019989322228511, "edger_log2fc": 2.52413400275062, "edger_q": 3.0990077190244e-06 } ] }, { "candidate": "BdSGR9", "pathway": "Amyloplast Sedimentation", "arabidopsis_gene": "SGR9", "arabidopsis_agi": "AT5G02750", "anchor_status": "verified: UniProt Q8GXF8 (SGR9 At5g02750 F9G14.60); corrected on 2026-10-14 from AT1G17400, which is LAZY2/DRO3", "brachypodium_orthologs": "BRADI_2g25560v3", "brachypodium_homology": "one2one", "rice_orthologs": "Os05g0408800", "wheat_orthologs": "TraesCS1A02G255600 TraesCS1B02G266300 TraesCS1D02G254900", "ortholog_note": "", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdSGR2", "pathway": "Amyloplast Sedimentation", "arabidopsis_gene": "SGR2", "arabidopsis_agi": "AT1G31480", "anchor_status": "verified: UniProt Q8W5R2 (SGR2 At1g31480 F27M3.29); corrected on 2026-10-14 from AT2G46870, which is NGA1", "brachypodium_orthologs": "BRADI_3g13467v3", "brachypodium_homology": "one2one", "rice_orthologs": "Os08g0110700", "wheat_orthologs": "TraesCS7A02G320600 TraesCS7B02G221600 TraesCS7D02G317500", "ortholog_note": "", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdTIR1", "pathway": "Auxin Receptor", "arabidopsis_gene": "TIR1", "arabidopsis_agi": "AT3G62980", "anchor_status": "verified: UniProt Q570C0 (TIR1 FBL1 WEI1)", "brachypodium_orthologs": "BRADI_2g35720v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os05g0150500", "wheat_orthologs": "TraesCS1A02G091300 TraesCS1B02G119100 TraesCS1D02G099900", "ortholog_note": "", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdAFB2", "pathway": "Auxin Receptor", "arabidopsis_gene": "AFB2", "arabidopsis_agi": "AT3G26810", "anchor_status": "verified: UniProt Q9LW29 (AFB2 LRF2 At3g26810); corrected on 2026-10-14 from AT4G03190, which is GRH1/AFB1", "brachypodium_orthologs": "BRADI_4g18220v3 BRADI_5g08680v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os04g0395600 Os11g0515500", "wheat_orthologs": "TraesCS2A02G286200 TraesCS2B02G302900 TraesCS2D02G285000 TraesCS5A02G281100 TraesCS5B02G280100 TraesCS5D02G288000", "ortholog_note": "", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdARF7", "pathway": "Auxin Response Factor", "arabidopsis_gene": "ARF7", "arabidopsis_agi": "AT5G20730", "anchor_status": "verified: UniProt P93022 (ARF7 BIP IAA21)", "brachypodium_orthologs": "BRADI_1g46602v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os06g0196700", "wheat_orthologs": "TraesCS7A02G160800 TraesCS7B02G065800 TraesCS7D02G161900", "ortholog_note": "Brachypodium ortholog(s) shared with BdARF19", "su2023_deg_calls": 2, "su2023_degs": "Gaz8 shoot +0.54 (BRADI_3g40437v3, Su et al. best hit); Gaz8 shoot +0.99 (BRADI_1g34340v3, Su et al. best hit)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_3g40437v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": 0.538821656458611, "deseq_padj": 0.0070565899317335, "edger_log2fc": 0.516216232795767, "edger_q": 0.0082101307468347 }, { "brachypodium_gene_id": "BRADI_1g34340v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": 0.985499712553853, "deseq_padj": 3.7770899390739006e-10, "edger_log2fc": 0.962657340321281, "edger_q": 1.62113656761612e-07 } ] }, { "candidate": "BdARF19", "pathway": "Auxin Response Factor", "arabidopsis_gene": "ARF19", "arabidopsis_agi": "AT1G19220", "anchor_status": "verified: UniProt Q8RYC8 (ARF19 IAA22 At1g19220)", "brachypodium_orthologs": "BRADI_1g46602v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os06g0196700", "wheat_orthologs": "TraesCS7A02G160800 TraesCS7B02G065800 TraesCS7D02G161900", "ortholog_note": "Brachypodium ortholog(s) shared with BdARF7", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdIAA14", "pathway": "Aux/IAA Repressor", "arabidopsis_gene": "IAA14", "arabidopsis_agi": "AT4G14550", "anchor_status": "verified: UniProt Q38832 (IAA14 SLR1 At4g14550); corrected on 2026-10-14 from AT4G14560, which is IAA1", "brachypodium_orthologs": "BRADI_1g09090v3 BRADI_1g14240v3 BRADI_1g36930v3 BRADI_2g04910v3 BRADI_2g34030v3 BRADI_4g02600v3 BRADI_4g35960v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os01g0178500 Os03g0633500 Os03g0742900 Os05g0178600 Os12g0601300", "wheat_orthologs": "TraesCS1A02G118400 TraesCS1B02G138100 TraesCS1D02G119500 TraesCS3A02G121300 TraesCS3B02G140700 TraesCS3D02G123400 TraesCS5A02G058600 TraesCS5A02G378300 TraesCS5A02G382600 TraesCS5B02G058500 TraesCS5B02G381900 TraesCS5B02G386800 TraesCS5D02G069300 TraesCS5D02G388300 TraesCS5D02G392000 TraesCS7A02G371500 TraesCS7B02G256100 TraesCS7D02G351400", "ortholog_note": "", "su2023_deg_calls": 1, "su2023_degs": "Gaz8 shoot +0.44 (BRADI_2g34030v3, Compara)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_2g34030v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_many2many", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": 0.444669267982936, "deseq_padj": 0.004014953536414, "edger_log2fc": 0.422123387268013, "edger_q": 0.039760134450063 } ] }, { "candidate": "BdPGM1", "pathway": "Statolith Starch Biosynthesis", "arabidopsis_gene": "PGM", "arabidopsis_agi": "AT5G51820", "anchor_status": "verified: UniProt Q9SCY0 (PGMP PGM RGV2)", "brachypodium_orthologs": "BRADI_3g22930v3", "brachypodium_homology": "one2one", "rice_orthologs": "Os10g0189100", "wheat_orthologs": "", "ortholog_note": "", "su2023_deg_calls": 1, "su2023_degs": "Gaz8 shoot -0.52 (BRADI_3g22930v3, Compara)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_3g22930v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_one2one", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": -0.51815948643587, "deseq_padj": 8.76706112299021e-05, "edger_log2fc": -0.54116144377338, "edger_q": 0.0053764228935469 } ] }, { "candidate": "BdADG1", "pathway": "Statolith Starch Biosynthesis", "arabidopsis_gene": "ADG1", "arabidopsis_agi": "AT5G48300", "anchor_status": "verified: UniProt P55228 (APS1 ADG1 APS); corrected on 2026-10-14 from AT5G19220, which is ADG2/APL1", "brachypodium_orthologs": "BRADI_3g22330v3 BRADI_4g27570v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os08g0345800 Os09g0298200", "wheat_orthologs": "TraesCS5B02G175800 TraesCS5D02G182600 TraesCS7A02G287400 TraesCS7B02G183300 TraesCS7D02G284900", "ortholog_note": "", "su2023_deg_calls": 1, "su2023_degs": "Bd21 shoot +1.21 (BRADI_4g27570v3, Compara)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_4g27570v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_one2many", "accession": "Bd21", "organ": "shoot", "deseq_log2fc": 1.21114387534537, "deseq_padj": 0.0120413480914202, "edger_log2fc": 1.23500602877519, "edger_q": 0.0014613451853981 } ] }, { "candidate": "BdCPK28", "pathway": "Calcium Signaling Kinase", "arabidopsis_gene": "CPK28", "arabidopsis_agi": "AT5G66210", "anchor_status": "verified: UniProt Q9FKW4 (CPK28 At5g66210 K2A18.29)", "brachypodium_orthologs": "BRADI_1g52567v3 BRADI_3g02600v3", "brachypodium_homology": "many2many", "rice_orthologs": "Os02g0126400 Os07g0409900", "wheat_orthologs": "TraesCS2A02G239900 TraesCS2D02G245700 TraesCS6A02G089400 TraesCS6B02G111800 TraesCSU02G016900", "ortholog_note": "", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdCAS", "pathway": "Calcium Sensing Receptor", "arabidopsis_gene": "CAS", "arabidopsis_agi": "AT5G23060", "anchor_status": "verified: UniProt Q9FN48 (CAS STR3 At5g23060)", "brachypodium_orthologs": "BRADI_3g56190v3", "brachypodium_homology": "one2one", "rice_orthologs": "Os02g0729400", "wheat_orthologs": "TraesCS6A02G290600 TraesCS6B02G320900 TraesCS6D02G271900", "ortholog_note": "", "su2023_deg_calls": 2, "su2023_degs": "Bd21 shoot -0.88 (BRADI_3g56190v3, Compara); Gaz8 shoot -0.69 (BRADI_3g56190v3, Compara)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_3g56190v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_one2one", "accession": "Bd21", "organ": "shoot", "deseq_log2fc": -0.881389936397832, "deseq_padj": 0.001292068892762, "edger_log2fc": -0.850000838082249, "edger_q": 0.0009799474077161 }, { "brachypodium_gene_id": "BRADI_3g56190v3", "match": "Compara ortholog of the anchor", "compara_homology_type": "ortholog_one2one", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": -0.68510508061111, "deseq_padj": 2.27383232939531e-07, "edger_log2fc": -0.706854407006818, "edger_q": 0.0002109333771422 } ] }, { "candidate": "BdCRK28", "pathway": "Receptor-like Kinase", "arabidopsis_gene": "CRK28", "arabidopsis_agi": "AT4G21400", "anchor_status": "verified: UniProt O65405 (CRK28 At4g21400 F18E5.20); corrected on 2026-10-14 from AT3G55950, which is CCR3/CRR3", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdCML24", "pathway": "Calmodulin-Like Protein", "arabidopsis_gene": "CML24", "arabidopsis_agi": "AT5G37770", "anchor_status": "verified: UniProt P25070 (CML24 TCH2 At5g37770); corrected on 2026-10-14 from AT5G15060, which is LBD34/ASL42", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 1, "su2023_degs": "Gaz8 shoot +0.62 (BRADI_2g02340v3, Su et al. best hit)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_2g02340v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": 0.619267534749236, "deseq_padj": 0.0096798398153057, "edger_log2fc": 0.595312361799973, "edger_q": 0.0041059127301132 } ] }, { "candidate": "BdMSL10", "pathway": "Mechanosensitive Ion Channel", "arabidopsis_gene": "MSL10", "arabidopsis_agi": "AT5G12080", "anchor_status": "verified: UniProt Q9LYG9 (MSL10 At5g12080 F14F18.230); corrected on 2026-10-14 from AT4G00290, which is MSL1", "brachypodium_orthologs": "BRADI_1g46387v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os06g0205600", "wheat_orthologs": "TraesCS7A02G166500 TraesCS7B02G070900 TraesCS7D02G167000", "ortholog_note": "", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdEXPA1", "pathway": "Cell Wall Loosening (Expansin)", "arabidopsis_gene": "EXPA1", "arabidopsis_agi": "AT1G69530", "anchor_status": "verified: UniProt Q9C554 (EXPA1 EXP1 At1g69530); corrected on 2026-10-14 from AT2G39700, which is EXPA4/EXP4", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 3, "su2023_degs": "Bd21-3 shoot +0.88 (BRADI_2g22290v3, Su et al. best hit); Gaz8 shoot +0.86 (BRADI_2g22290v3, Su et al. best hit); Gaz8 shoot +1.21 (BRADI_3g59460v3, Su et al. best hit)", "spaceflight_degs": [ { "brachypodium_gene_id": "BRADI_2g22290v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Bd21-3", "organ": "shoot", "deseq_log2fc": 0.876911640643292, "deseq_padj": 0.0110213868814893, "edger_log2fc": 0.888363417503839, "edger_q": 0.0093330450550443 }, { "brachypodium_gene_id": "BRADI_2g22290v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": 0.858046151623976, "deseq_padj": 0.0258270665034008, "edger_log2fc": 0.836242171475355, "edger_q": 9.24203547293981e-06 }, { "brachypodium_gene_id": "BRADI_3g59460v3", "match": "Su et al. best-hit Arabidopsis ortholog is the anchor", "compara_homology_type": "", "accession": "Gaz8", "organ": "shoot", "deseq_log2fc": 1.20852133442499, "deseq_padj": 7.73665060078525e-07, "edger_log2fc": 1.18487608545078, "edger_q": 5.82779265421328e-09 } ] }, { "candidate": "BdXTH1", "pathway": "Xyloglucan Transglucosylase", "arabidopsis_gene": "XTH1", "arabidopsis_agi": "AT4G13080", "anchor_status": "verified: UniProt Q9SV61 (XTH1 At4g13080 F25G13.170); corrected on 2026-10-14 from AT4G14130, which is XTH15/XTR7", "brachypodium_orthologs": "BRADI_1g44777v3", "brachypodium_homology": "one2many", "rice_orthologs": "Os06g0237400", "wheat_orthologs": "TraesCS3A02G083900 TraesCS3B02G099000 TraesCS7A02G194300 TraesCS7B02G099900 TraesCS7D02G195900", "ortholog_note": "", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] }, { "candidate": "BdCSLD1", "pathway": "Cellulose/Glucan Synthase", "arabidopsis_gene": "CSLD1", "arabidopsis_agi": "AT2G33100", "anchor_status": "verified: UniProt O49323 (CSLD1 At2g33100 F25I18.16); corrected on 2026-10-14 from AT4G25810, which is XTH23/XTR6", "brachypodium_orthologs": "", "brachypodium_homology": "", "rice_orthologs": "", "wheat_orthologs": "", "ortholog_note": "TODO: no Brachypodium ortholog in Ensembl Compara (plants)", "su2023_deg_calls": 0, "su2023_degs": "", "spaceflight_degs": [] } ] }