gene tree
Built FastTree trees for PAL, LAMT, and NCS from Lamiales/Lamiaceae and internal controls.
Methods, boundaries and provenance
Pathway evidence language
Definitions used across the atlas, family, species, candidate and expression pages. Evidence states describe the released database records and do not replace experimental validation.
Status language
Do not conflate evidence states
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Stable locus evidence
A concrete, species-linked candidate identifier is available in the public pathway package. It is still a computational candidate, not a validated biochemical function.
□ᴿ
Reference-only family summary
A family-level assignment count or reference-library module is available, but no individual stable candidate ID is asserted.
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ND — Not detected
A candidate-to-expression mapping exists, but no valid quantitative value was detected in the released expression matrix. ND is distinct from numeric zero.
⊘
Unavailable
The required data are not available in this release. Unavailable never means biological absence.
Evidence modes
How candidate and family records are represented
Gene-tree evidenceCandidate identifiers from the bundled gene-tree workflow, with BLAST/HMM evidence fields retained when available.
Candidate IDs
Motif-screen evidenceCandidate identifiers screened with motif proxies. Motif presence does not establish substrate or enzyme activity.
Proxy evidence
Family-count evidenceSpecies-level assignment counts without individual candidate identifiers. The UI retains counts without fabricating locus IDs.
Reference-only
Local 100-kb clustering proxyA coordinate-based local clustering summary. It is not full cross-species synteny.
Structural proxy
Validation status
Evidence layers in the bundled release
Completed
domain proxy
Evaluated motif proxies for TPS, CYP76, BAHD, and RAS using local candidate protein sequences.
local cluster proxy
Computed 100-kb local clustering/tandem-like proxy for key families in top Lamiales species with local GFF annotations.
plantsme five pathways
PlantSME full-mode identification of alkaloid, flavonoid, phenylpropanoid, steroid and terpenoid enzyme-family candidates using genome-derived proteins or transcriptome-derived substitutes with explicit provenance.
Partial
synteny
MCScanX/jcvi were not available locally; completed coordinate-based local clustering proxy instead of full cross-species synteny.
Not available locally
expression
No clear local expression atlas / RNA quantification tables were found in the repository.
metabolome
No clear local metabolomics tables were found in the repository.
Expression & ND
Quantitative display rules
Species-level transcriptome matrix summaries are shown independently. Candidate IDs are not joined to expression IDs because annotation versions do not map directly.
- Measured values use a numeric legend and a diverging row z-score scale centred at zero.
- ND cells use an independent hatch pattern and never occupy the low end of the continuous scale.
- An all-ND matrix remains visible with an explicit warning; it is not converted into “no expression data”.
- Unmapped candidate IDs remain separate from mapped-but-ND identifiers.
Re-identification provenance
Patched-library source profiles
The following provenance rows are included in the release and displayed without inferring missing values.
| Species | Valid proteins | Accepted modules | Assignments | Library | Mode |
|---|---|---|---|---|---|
| Agastache foeniculum | 34,056 | 91 | 3,535 | 20260604-patched | full |
| Agastache rugosa | 26,430 | 90 | 3,820 | 20260604-patched | full |
| Ajuga decumbens | 36,055 | 92 | 5,916 | 20260604-patched | full |
| Ajuga reptans | 36,601 | 92 | 3,814 | 20260604-patched | full |
| Ballota pseudodictamnus | 44,190 | 90 | 4,067 | 20260604-patched | full |
| Callicarpa americana | 62,993 | 90 | 9,726 | 20260604-patched | full |
| Callicarpa nudiflora | 31,266 | 90 | 4,672 | 20260604-patched | full |
| Clerodendrum bungei | 41,434 | 92 | 3,889 | 20260604-patched | full |
| Clinopodium barosmum | 41,864 | 91 | 6,190 | 20260604-patched | full |
| Clinopodium gracile | 40,083 | 91 | 4,749 | 20260604-patched | full |
| Collinsonia canadensis | 49,336 | 92 | 4,600 | 20260604-patched | full |
| Congea tomentosa | 41,401 | 90 | 3,934 | 20260604-patched | full |
| Cornutia pyramidata | 73,850 | 99 | 5,024 | 20260604-patched | full |
| Dracocephalum rupestre | 35,602 | 89 | 5,366 | 20260604-patched | full |
| Drepanocaryum sewerzowii | 26,957 | 93 | 3,367 | 20260604-patched | full |
| Elsholtzia splendens | 55,748 | 88 | 8,810 | 20260604-patched | full |
| Glechoma hederacea | 45,148 | 94 | 4,523 | 20260604-patched | full |
| Glechoma longituba | 34,930 | 92 | 5,620 | 20260604-patched | full |
| Gmelina philippensis | 37,915 | 93 | 3,711 | 20260604-patched | full |
| Holmskioldia sanguinea | 42,679 | 94 | 4,118 | 20260604-patched | full |
| Hyptis suaveolens | 40,037 | 93 | 4,252 | 20260604-patched | full |
| Hyssopus officinalis | 50,669 | 89 | 7,619 | 20260604-patched | full |
| Isodon lophanthoides | 35,863 | 89 | 5,065 | 20260604-patched | full |
| Isodon serra | 27,867 | 91 | 4,397 | 20260604-patched | full |
| Lamium album | 39,532 | 93 | 3,861 | 20260604-patched | full |
| Lavandula angustifolia | 44,101 | 90 | 4,270 | 20260604-patched | full |
| Leonotis leonurus | 34,946 | 89 | 3,459 | 20260604-patched | full |
| Leonurus cardiaca | 32,032 | 88 | 3,488 | 20260604-patched | full |
| Leonurus japonicus | 28,652 | 91 | 3,974 | 20260604-patched | full |
| Leonurus sibiricus | 25,733 | 90 | 3,700 | 20260604-patched | full |
| Lycopus americanus | 40,879 | 94 | 3,745 | 20260604-patched | full |
| Marmoritis complanata | 28,336 | 92 | 4,158 | 20260604-patched | full |
| Marrubium vulgare | 33,432 | 91 | 3,572 | 20260604-patched | full |
| Melissa officinalis | 32,458 | 92 | 3,567 | 20260604-patched | full |
| Mentha longifolia | 20,031 | 89 | 3,110 | 20260604-patched | full |
| Mentha spicata | 40,191 | 92 | 4,091 | 20260604-patched | full |
| Mentha x piperita | 43,736 | 92 | 4,584 | 20260604-patched | full |
| Monarda didyma | 34,278 | 90 | 3,860 | 20260604-patched | full |
| Mosla chinensis | 32,297 | 89 | 4,711 | 20260604-patched | full |
| Mosla soochowensis | 34,133 | 87 | 4,643 | 20260604-patched | full |
| Nepeta cataria | 78,876 | 93 | 11,518 | 20260604-patched | full |
| Nepeta mussinii | 42,874 | 86 | 6,581 | 20260604-patched | full |
| Ocimum basilicum | 78,990 | 93 | 13,073 | 20260604-patched | full |
| Ocimum tenuiflorum | 36,427 | 92 | 5,457 | 20260604-patched | full |
| Origanum majorana | 50,827 | 96 | 4,338 | 20260604-patched | full |
| Origanum vulgare | 44,141 | 91 | 5,362 | 20260604-patched | full |
| Perilla citriodora | 23,675 | 86 | 3,737 | 20260604-patched | full |
| Perilla frutescens | 38,941 | 89 | 6,318 | 20260604-patched | full |
| Perilla frutescens var. hirtella | 23,675 | 86 | 3,737 | 20260604-patched | full |
| Perovskia atriplicifolia | 35,771 | 90 | 3,864 | 20260604-patched | full |
| Petraeovitex bambusetorium | 42,920 | 93 | 4,023 | 20260604-patched | full |
| Phlomis fruticosa | 58,479 | 93 | 4,750 | 20260604-patched | full |
| Phlomoides rotata | 51,686 | 97 | 6,581 | 20260604-patched | full |
| Plectranthus barbatus | 46,489 | 93 | 5,031 | 20260604-patched | full |
| Pogostemon cablin | 132,407 | 99 | 19,603 | 20260604-patched | full |
| Premna microphylla | 45,762 | 91 | 4,236 | 20260604-patched | full |
| Prostanthera lasianthos | 46,730 | 92 | 4,077 | 20260604-patched | full |
| Prunella vulgaris | 45,001 | 91 | 5,478 | 20260604-patched | full |
| Rotheca myricoides | 59,312 | 93 | 5,201 | 20260604-patched | full |
| Salvia bowleyana | 44,032 | 90 | 4,364 | 20260604-patched | full |
| Salvia divinorum | 38,973 | 92 | 5,686 | 20260604-patched | full |
| Salvia hispanica | 46,507 | 90 | 7,399 | 20260604-patched | full |
| Salvia miltiorrhiza | 29,236 | 89 | 4,409 | 20260604-patched | full |
| Salvia officinalis | 36,084 | 92 | 3,769 | 20260604-patched | full |
| Salvia rosmarinus | 51,386 | 91 | 6,912 | 20260604-patched | full |
| Salvia sclarea | 17,186 | 89 | 2,166 | 20260604-patched | full |
| Salvia splendens | 79,249 | 91 | 10,999 | 20260604-patched | full |
| Schizonepeta tenuifolia | 27,971 | 86 | 3,878 | 20260604-patched | full |
| Scutellaria baicalensis | 30,090 | 91 | 4,520 | 20260604-patched | full |
| Scutellaria barbata | 34,557 | 92 | 4,065 | 20260604-patched | full |
| Stachys officinalis | 70,031 | 93 | 4,344 | 20260604-patched | full |
| Stenogyne calaminthoides | 77,090 | 95 | 9,969 | 20260604-patched | full |
| Tectona grandis | 35,551 | 94 | 5,913 | 20260604-patched | full |
| Teucrium canadense | 38,989 | 90 | 3,991 | 20260604-patched | full |
| Teucrium chamaedrys | 128,013 | 97 | 19,012 | 20260604-patched | full |
| Teucrium marum | 73,466 | 90 | 10,387 | 20260604-patched | full |
| Thymus quinquecostatus | 29,676 | 90 | 4,704 | 20260604-patched | full |
| Thymus vulgaris | 52,878 | 95 | 4,585 | 20260604-patched | full |
| Vitex agnus-castus | 42,689 | 92 | 4,472 | 20260604-patched | full |
| Westringia fruticosa | 40,051 | 91 | 3,750 | 20260604-patched | full |
Known limitations
Interpretation boundaries
Candidate function
Computational enzyme-family candidates and genome-structure support, not validated biochemical function.
Synteny
Local 100-kb clustering proxy, not full cross-species synteny.
Coverage
Only 80 of 808 database species currently expose public candidate identifiers. Missing profiles are not interpreted as pathway absence.
Public sequence boundary
Candidate source fields may include protein length, but public protein sequence records are not released by the current LamiOmicsDB interface.