Add missing 2023 records

Glycine/max/studies/glyma.Lu_Zhao_2017.yml

@@ -93,7 +93,8 @@ confidence: 5
 curators:
   - Steven Cannon
 phenotype_synopsis: Photoperiodic flowering time regulation
-comments: Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean
+comments:
+  - Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean
 traits:
   - entity_name: flowering time
     entity: TO:0002616

Glycine/max/studies/glyma.Wang_Li_2021.yml

@@ -13,7 +13,6 @@ comments:
     "LOCUS NP_001242439"
   - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height
   - glyma.Wm82.gnm2.ann1.Glyma.13G287600.1 also works
-  -
 phenotype_synopsis: Negatively correlated with shoot length and trailing growth
 traits:
   - entity_name: plant height

Glycine/soja/gene_functions/glyso.citations.txt

@@ -0,0 +1,2 @@
+10.1111/pbi.13536	33368860	PMC8196659	Jin, Sun et al., 2021	"Jin T, Sun Y, Shan Z, He J, Wang N, Gai J, Li Y. Natural variation in the promoter of GsERD15B affects salt tolerance in soybean. Plant Biotechnol J. 2021 Jun;19(6):1155-1169. doi: 10.1111/pbi.13536. Epub 2021 Jan 19. PMID: 33368860; PMCID: PMC8196659."
+10.1038/ncomms5340	25004933	PMC4104456	Qi, Li et al., 2014	"Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, Isobe S, Wong CF, Wong KS, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang TH, Liu X, Tong SW, Chan TF, Yiu SM, Tabata S, Wang J, Xu X, Lam HM. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 2014 Jul 9;5:4340. doi: 10.1038/ncomms5340. PMID: 25004933; PMCID: PMC4104456."

Glycine/soja/gene_functions/glyso.traits.yml

@@ -0,0 +1,60 @@
+## DOCUMENT 1 ##
+---
+scientific_name: Glycine soja
+gene_symbols:
+  - GsERD15B
+gene_symbol_long: Early Responsive to Dehydration 15B
+gene_model_pub_name: XP_028191281.1
+gene_model_full_id: glyso.PI483463.gnm1.ann1.GlysoPI483463.11G164100
+confidence: 4
+curators:
+  - Greg Murrell
+  - Steven Cannon
+  - Scott Kalberer
+comments:
+  - A seven-base pair deletion in the GsERD15B promoter was discovered in the majority (42) of the 48 wild Glycine soja accessions with enhanced salt tolerance.
+  - Increased expression of GsERD15B in response to salt stress was associated with up-regulation of two GmPAB genes (GmPAB-14G and GmPAB-17G) and known stress-related genes including ABA-related genes (GmABI1, GmABI2, GmbZIP1), a proline synthesis-related gene (GmP5CS), a catalase peroxidase gene (GmCAT4), water loss-related genes (GmPIP1:6, GmMYB84), and an ion exchanger encoding gene (GmSOS1).
+  - GsERD15B overexpression enhanced the promoter activities of GmABI2, GmP5CS and GmbZIP1 in tobacco leaf assays.
+  - GsERD15B encodes an ERD15 protein with transcriptional activation function.  The ERD15 contains a conserved PAM2 domain in the N-terminus that mediates its interaction with the PABC domain of poly(A)-binding (PAB) proteins.
+phenotype_summary: Gene overexpression in Glycine enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport.
+traits:
+  - entity_name: salt tolerance
+    entity: TO:0006001
+  - relation_name: positively regulates
+    relation: RO:0002213
+references:
+  - citation: Jin, Sun et al., 2021
+    doi: 10.1111/pbi.13536
+    pmid: 33368860
+
+
+## DOCUMENT 2 ##
+---
+scientific_name: Glycine soja
+gene_symbols:
+  - GmCHX1
+gene_symbol_long: cation/H(+) antiporter 1
+gene_model_pub_name: Glysoja01g005509
+gene_model_full_id: glyso.PI483463.gnm1.ann1.GlysoPI483463.03G135400
+confidence: 4
+comments:
+  - Gene Glysoja01g005509 is newly sequenced from Glycine soja W05 and is not in the annotation glyso.W05.gnm1.ann1.
+  - The newly named gene Glysoja01g005509 has a different format than others in that annotation, which have a dot, e.g. Glysoja.01G001001
+  - The gene GmCHX1 is associated with salt tolerance in Glycine soja W05
+  - The gene glyso.PI483463.gnm1.ann1.GlysoPI483463.03G135400 has a full-length 100% match with the reported Glysoja01g005509
+  - The reported sequence is >KF879911.1 Glycine soja CHX1 mRNA, complete cds ATGACGTTCAACGCGAGCACCATCACAACGGCGTCGGAAGGAGCCTGGCAGGGCGATAATCCCCTGAACC ACGCTCTTCCTTTGTTGATCGTTCAAACCATCCTCGTAGTCTTCGTGAGCCGCACACTCGCCTTTCTCCT CAAACCCTTTCGTCAACCTAAAGTTGTCGCCGAGATTATTGGTGGAATTTTGTTGGGGCCTTCTGCTATT GGGCGCAACAAGAAATTCATGCACATAGTGTTCCCAGCATGGAGCACTACCATGCTGGAATCAGTGGCAA GCTTCGGCCTCTTATTCTATCTATTTCTGGTGGGCCTAGAGCTCGACTTTCGCACCATTCGCCGGAGCGG CAAGCAAGCCTTCAACATCGCGGTGGCCGGAATAACCCTCCCCTTCATCTGCGCCGTGGGAGTAACGTTC CTTCTCCAGAGAGCCATCCGCTCTGAAAACCATAACATAGGGTACGTTCAGCACTTCGTGTTCTTAGGGG TATCTCTGTCCATCACGGCTTTCCCTGTGCTCGCGCGCATCTTAGCGGAGCTCAAACTGCTGACCACACG TGTGGGAGAAACCGCCATGGCGGCTGCAGCCTTCAACGACGTCGCTGCGTGGGTTTTGTTGGCCTTGGCG GTGGCTTTGGCTGGCCAGGGACACAAAAGCAGCTTGTTGACATCAATATGGGTGCTCTTCTCAGGGATGG CGTTTGTTGCAGCCATGATGATCCTGGTTCGACCGGTGATGAACCGTGTTGCTCGCAAGTGTTCTCACGA ACAAGACGTGTTACCCGAAATCTACATATGTTTAACTCTAGCGGGAGTAATGTTATCGGGGTTAGTGACA GACATGATAGGGTTACATTCAATTTTCGGGGGATTTGTTTTCGGGCTAACGATACCGAAAGGTGGCGAAT TTGCAAATAGAATGACGAGGAGGATTGAGGACTTCGTGTCCACGTTGTTCCTTCCCTTGTACTTTGCTGC CAGTGGTTTGAAAACTGACGTGACTAAGTTACGAAGCGTGGTGGATTGGGGGCTTCTTTTGCTGGTTACG TCCACCGCGAGCGTGGGGAAGATTTTGGGAACGTTTGCGGTGGCGATGATGTGCATGGTGCCGGTGAGAG AATCCTTGACGCTTGGAGTGTTAATGAACACCAAAGGGTTGGTGGAGCTAATCGTTCTCAATATTGGCAG AGAGAAGAAGGTGCTTAACGACGAGATGTTTACCATCCTAGTACTCATGGCTCTCTTCACCACCTTCATT ACAACTCCAATAGTCTTGGCCATATACAAACCCTCTCGTATAGTAAACTCCGGTTCGCAAAAACCGTCGC GGCTAACAGATTTGCAAGAGAAGCTTCGCATTCTTGCGTGCATCCATGGACCTGGCAACATACCCTCACT AATCAACTTCGTTGAATCAATTCGGGCCACCAACATGTCACGACTCAAACTCTACGTGATGCAACTTACC GAACTCACTGATAGCTCTTCCTCCATCTTGATGGTTCAACGCAGTCGAAAGAATGGTTTTCCCTTCATCA ACCGAATGAAGAGTGGACCAATGCATGAGCAAATTGCCACAGCATTCCAGGCTTATGGTGAAGTGGGTAA AGTTACTGTGCATCATTTAACATCTATCTCTCTATTGTCAACAATGCACGAGGACATATGCCACGTTGCA GAAAAGAAAGGTGTGGCAATGATTATATTGCCCTTCCACAAAAGGTGGGGAGGGGAAGATGAAGAGGTGA CAGAAGACTTAGGGCAGGGTTTGAGGGAAGTCAATCAAAGGGTGCTTCAAAATGCAGCCTGCTCTGTCGC AGTGCTAGTCAATCGTGGGGTTGCCAGAAGGTACGAACAAGAACCTGAGACAAGTGTTGCTGCAAGGAAA AGAGTGTGCATAATTTTCATTGGTGGACCACATGATCGCAAGGTTTTGGAGTTAGGTAGCAGAATGGCAG AGCATCCAGCAATTAGGTTGCTTTTAGTGAGATTCACTTCATACACAGAAGTTGGGGACGAGGGACCCAA ATATAACTCACCAACATCAACCACCAACTGGGAAAAAGAAAAGGAGTTGGATGAGGAAGCAGTAAACGAG TTCAAGGTTAAATGGCAGGAGACTGTGGAGTACATTGAAAAGAACGCAACCAACATAACAGAGGAGGTGT TATCAATTGGGAAAGCTAAGGATCACGACCTAGTAATTGTGGGGAAGCAACAACTTGAGACAACCATGTT GACAAACATAGATTTTCGTCACGGGAATGAAGAGCTGGGACCCATTGGAGATCTCTTTGTCTCTTCGGGT AACGGCATTACCAGTTCATTGCTCGTTATACAGGACCGATATTTTATAAATTCAAACGAAAGTAATCTCG TTAAGACATCAAGGGCCGAGAGTACTGTGATTAAAGATGCTATCGAAGAACTTTAA
+  - Protein product >AIG92838.1 CHX1 [Glycine soja] MTFNASTITTASEGAWQGDNPLNHALPLLIVQTILVVFVSRTLAFLLKPFRQPKVVAEIIGGILLGPSAI GRNKKFMHIVFPAWSTTMLESVASFGLLFYLFLVGLELDFRTIRRSGKQAFNIAVAGITLPFICAVGVTF LLQRAIRSENHNIGYVQHFVFLGVSLSITAFPVLARILAELKLLTTRVGETAMAAAAFNDVAAWVLLALA VALAGQGHKSSLLTSIWVLFSGMAFVAAMMILVRPVMNRVARKCSHEQDVLPEIYICLTLAGVMLSGLVT DMIGLHSIFGGFVFGLTIPKGGEFANRMTRRIEDFVSTLFLPLYFAASGLKTDVTKLRSVVDWGLLLLVT STASVGKILGTFAVAMMCMVPVRESLTLGVLMNTKGLVELIVLNIGREKKVLNDEMFTILVLMALFTTFI TTPIVLAIYKPSRIVNSGSQKPSRLTDLQEKLRILACIHGPGNIPSLINFVESIRATNMSRLKLYVMQLT ELTDSSSSILMVQRSRKNGFPFINRMKSGPMHEQIATAFQAYGEVGKVTVHHLTSISLLSTMHEDICHVA EKKGVAMIILPFHKRWGGEDEEVTEDLGQGLREVNQRVLQNAACSVAVLVNRGVARRYEQEPETSVAARK RVCIIFIGGPHDRKVLELGSRMAEHPAIRLLLVRFTSYTEVGDEGPKYNSPTSTTNWEKEKELDEEAVNE FKVKWQETVEYIEKNATNITEEVLSIGKAKDHDLVIVGKQQLETTMLTNIDFRHGNEELGPIGDLFVSSG NGITSSLLVIQDRYFINSNESNLVKTSRAESTVIKDAIEEL
+curators:
+  - Greg Murrell, Steven Cannon
+phenotype_summary: Raises salt tolerance.
+traits:
+  - entity_name: salt tolerance
+    entity: TO:0006001
+  - relation_name: positively regulates
+    relation: RO:0002213
+references:
+  - citation: Qi, Li et al., 2014
+    doi: 10.1038/ncomms5340
+    pmid: 25004933
+
+

Lotus/japonicus/gene_functions/lotja.citations.txt

@@ -0,0 +1,4 @@
+10.1093/pcp/pcu168	25416287	null	Soyano, Shimoda et al., 2015	"Soyano T, Shimoda Y, Hayashi M. NODULE INCEPTION antagonistically regulates gene expression with nitrate in Lotus japonicus. Plant Cell Physiol. 2015 Feb;56(2):368-76. doi: 10.1093/pcp/pcu168. Epub 2014 Nov 20. PMID: 25416287."
+10.1104/pp.113.233379	24722550	PMC4043699	Yoro, Suzaki et al., 2014	"Yoro E, Suzaki T, Toyokura K, Miyazawa H, Fukaki H, Kawaguchi M. A Positive Regulator of Nodule Organogenesis, NODULE INCEPTION, Acts as a Negative Regulator of Rhizobial Infection in Lotus japonicus. Plant Physiol. 2014 Jun;165(2):747-758. doi: 10.1104/pp.113.233379. Epub 2014 Apr 10. PMID: 24722550; PMCID: PMC4043699."
+10.1073/pnas.1412716111	25246578	PMC4210044	Soyano, Hirakawa et al., 2014	"Soyano T, Hirakawa H, Sato S, Hayashi M, Kawaguchi M. Nodule Inception creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production. Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14607-12. doi: 10.1073/pnas.1412716111. Epub 2014 Sep 22. PMID: 25246578; PMCID: PMC4210044."
+10.1093/plcell/koab103	33826745	PMC8364233	Nishida, Nosaki et al., 2021	""

Lotus/japonicus/gene_functions/lotja.traits.yml

@@ -0,0 +1,41 @@
+## DOCUMENT 1 ##
+---
+scientific_name: Lotus japonicus
+gene_symbols:
+  - LjNIN
+gene_symbol_long: Nodule Inception
+gene_model_pub_name: Lj2G3V3373110
+gene_model_full_id: lotja.MG20.gnm3.ann1.Lj2G3V3373110
+confidence: 4
+curators:
+  - Marlene Dorneich-Hayes
+  - Scott Kalberer
+comments:
+  - Ectopic expression of Nodule Inception (LjNIN) produces nodule-like structures from the roots regardless of lack of rhizobia. Constitutive expression of NIN eventually leads to suppression of native NIN transcription in untransformed roots of the plant via effects on HAR1 receptor protein. The result is reduced nodulation and down-regulation of CLE-RS signal peptide expression.
+  - NIN codes for a transcription factor containing the RWP-RK domain that induces nodule primordia formation by promoting cortical cell division.
+  - NIN activates genes coding for the NIN-repressing signal proteins, Clavata3/Endosperm Surrounding Region Root Signal 1 (CLE-RS1) and CLE-RS2, that are expressed in the roots and travel long-distance to ultimately stop nodulation. They are perceived in the shoot by Hypernodulation Aberrant Root Formation 1 (HAR1) receptor proteins.
+phenotype_synopsis: LjNIN is part of an autoregulatory negative feedback loop in Lotus japonicus that maintains healthy numbers of nodules containing nitrogen-fixing rhizobia. NIN positively regulates rhizobium infection by inducing the genes necessary to establish the symbiosis when nitrate is limited.
+traits:
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - relation_name: negatively regulates
+    relation: RO:0002212
+  - entity_name: nodulation
+    entity: GO:0009877
+  - relation_name: positively regulates
+    relation: RO:0002213
+references:
+  - citation: Soyano, Hirakawa et al., 2014
+    doi: 10.1073/pnas.1412716111
+    pmid: 25246578
+  - citation: Soyano, Shimoda et al., 2015
+    doi: 10.1093/pcp/pcu168
+    pmid: 25416287
+  - citation: Yoro, Suzaki et al., 2014
+    doi: 10.1104/pp.113.233379
+    pmid: 24722550
+  - citation: Nishida, Nosaki et al., 2021
+    doi: 10.1093/plcell/koab103
+    pmid: 33826745
+
+