Arabidopsis pathways not yet curated

Back to the Arabidopsis corpus project.

Bottom line: of 107 Arabidopsis pathways checked, 34 have a module that
contains a reviewed Arabidopsis gene. These are mostly hormone signaling,
flowering, development and immunity. The other 73 are not curated for
Arabidopsis. 35 have no module at all. 21 have only a cross-kingdom module that
never mentions Arabidopsis. 17 have a module that mentions Arabidopsis but holds
none of our reviewed genes. Plant-specific metabolism is the largest gap: seven
of the nine hormone biosynthesis pathways, starch and sucrose,
flavonoids and anthocyanins, cuticle lipids, plastid lipids,
phytosterols, and nitrate and ammonium assimilation.

Method

Pathway list: ARATH-pathway-map.yaml is a
hand-curated map from 107 pathways to the modules that cover them. The list
draws on KEGG's 162 A. thaliana maps
(rest.kegg.jp/list/pathway/ath,
retrieved 2026-10-19) and adds well-known plant processes that KEGG has no
map for (cold acclimation, karrikin, UV-B, small-RNA pathways and others).
Modules were found by searching module titles and then reading each
module's scope. A module that covers only one step, or another lineage's
version of the chemistry (for example the bacterial nitrate reductase
module), is recorded as related_modules and does not count as coverage.
Script: scripts/arath_pathway_gaps.py
(uv run python projects/ARATH/scripts/arath_pathway_gaps.py). It fails if
a module id, gene folder or KEGG map in the map file does not exist. It
counts module members with the same rule as arath_corpus_stats.py.
Output: ARATH-pathway-gaps.yaml gives the
coverage call for each pathway, with module status, Arabidopsis members and
named genes that sit in no module.

Coverage calls:

Call	Meaning	Pathways
`NO_MODULE`	No module covers the pathway	35
`MODULE_WITHOUT_ARABIDOPSIS`	Module exists but never mentions Arabidopsis	21
`MODULE_WITHOUT_ARATH_GENES`	Module mentions Arabidopsis, has no reviewed ARATH gene	17
`MODULE_WITH_ARATH_GENES`	At least one reviewed ARATH gene is a module member	34

Limits. The pathway list is not exhaustive and has not been compared with
AraCyc/PMN. Of the 162 KEGG maps, 69 are assigned to a pathway and 32 are set
aside as overviews or animal/pathogen biology. The other 61 are not assessed;
they are general eukaryotic machinery (ribosome, spliceosome, proteasome, DNA
repair, N-glycosylation) or minor metabolic maps, and the output file lists
them. A MODULE_WITH_ARATH_GENES call does not mean the pathway is finished:
every module is still DRAFT, and some hold only one or two Arabidopsis genes. Two further limits of the script: mentions_arabidopsis is a plain substring
test, so a module that names Arabidopsis only in a caveat still counts as
mentioning it; and the output records the run date in summary.generated, so
re-running on another day changes that one field even when nothing else does.

1. No module (35)

Area	Pathways	Reviewed ARATH genes waiting for a module
Photosynthesis and carbon	Starch synthesis and degradation; sucrose synthesis and degradation
Hormone biosynthesis	Abscisic acid; auxin (TAA/YUCCA); cytokinin; brassinosteroid; jasmonate (oxylipin); ethylene; strigolactone	NCED3
Lipids	Plastid type II fatty acid synthesis; fatty acid desaturation; cutin, suberin and wax; galactolipids; phytosterols (cycloartenol route)	FAD2, CER1
Specialised metabolism	Flavonoids, flavonols and anthocyanins; indolic glucosinolates and their MYB regulation; mono-, sesqui- and triterpenoids	TT8, MYB34, MYB51, MYB122
Nitrogen	Nitrate assimilation; ammonium assimilation (GS/GOGAT)	CHL1
Cofactors and vitamins	Ascorbate (Smirnoff-Wheeler); tocopherol, plastoquinone and phylloquinone; molybdenum cofactor (eukaryotic)
Cell wall and sugars	Pectin, xyloglucan and callose; nucleotide sugar interconversion
Light and hormone signaling	Blue light (cryptochromes, phototropins); UV-B (UVR8); karrikin (KAI2)	UVR8
Abiotic stress	Cold acclimation (ICE1-CBF); drought (DREB2); phosphate starvation; iron deficiency; hypoxia (ERF-VII N-degron)	CBF1
Small RNA	siRNA, tasiRNA and RNA-directed DNA methylation
Organelles	Chloroplast protein import (TOC/TIC); autophagy

The last column lists named genes the script found in no module. Other
reviewed genes for these pathways sit in modules built for something else:
CRY1 and CRY2 (photomorphogenesis and photoperiod), RDR6 (miRNA biogenesis),
ICE1 (stomatal lineage) and DREB2A (heat stress).

2. Module exists but never mentions Arabidopsis (21)

These modules are generic or cross-kingdom. Arabidopsis representatives could
be added without writing new modules.

Central metabolism: glycolysis and gluconeogenesis, TCA cycle, pentose
phosphate pathway, oxidative phosphorylation, inositol phosphates,
trehalose 6-phosphate
Amino acids: branched-chain amino acids, histidine, polyamines, glutathione
Cofactors: MEP/mevalonate isoprenoid precursors, biotin, coenzyme A, NAD,
riboflavin, vitamin B6
Lipids: peroxisomal beta-oxidation, phospholipids (CDP-DAG), sphingolipids
Sulfate assimilation (APS reduction and PAPS activation)
Peroxisome biogenesis and matrix protein import

3. Module mentions Arabidopsis but holds no reviewed ARATH gene (17)

Photosynthesis: light reactions and antenna, Calvin-Benson-Bassham cycle,
chlorophyll biosynthesis (all parts of one photosynthesis module)
Cell wall: cellulose, xylan
Amino acids: shikimate and aromatic amino acids, aspartate family (Thr,
Met), proline and arginine catabolism, GABA shunt
Cofactors: thiamine, folate and one-carbon metabolism, siroheme
Other: glyoxylate cycle, Leloir galactose pathway, alcoholic fermentation,
ureide catabolism, ER unfolded protein response

4. Curated: module with reviewed ARATH genes (34)

These are hormone signaling (auxin, cytokinin, gibberellin, ABA, ethylene,
brassinosteroid, jasmonate, strigolactone, SA/NPR1), light and clock
(phytochrome, circadian), flowering and development (photoperiod,
vernalization, autonomous pathway, floral meristem and organ identity,
CLV-WUS, SHR-SCR, stomata, trichomes), immunity (FLS2/EFR, chitin, NLR), heat
and salt stress, and some metabolism (aliphatic glucosinolates, camalexin,
carotenes, gibberellin biosynthesis, fatty acid elongation, seed oil, lignin),
plus miRNA biogenesis, the LINC complex and photorespiration (the
photorespiration_c2_cycle module, with 18 reviewed Arabidopsis members as of
2026-10-20).

The thinnest are lignin (PAL1 only), seed oil (DGAT1 only), NLR immunity (EDS1
and PAD4; RPM1 and RPS2 are reviewed but are not members), the SOS pathway
(two members; HKT1 is reviewed but is not a member) and the carotene module,
which leaves out xanthophylls.

Suggested order

Plant-specific pathways in section 1. No other organism's curation fills
them, and several already have reviewed genes waiting: ABA biosynthesis
(NCED3), flavonoids/anthocyanins (TT8), cuticle (CER1), indolic
glucosinolates (MYB34/51/122), UV-B (UVR8), cold (CBF1).
Hormone biosynthesis as a set, so that every signaling module has its
matching biosynthesis module.
Starch and sucrose, together with Arabidopsis reviews for the
photosynthesis module (section 3).
Add Arabidopsis representatives to the section 2 modules.