Abstract
Abstract Orchidantha , the sole genus in the family Lowiaceae (Zingiberales), shows distinctive, orchid‐like flowers that emit a carrion‐like scent, attracting dung beetles for pollination. Despite their ecological and ornamental value, many Orchidantha species are endangered and face an elevated risk of extinction. Here, we present the first chromosome‐scale genome assembly of the endangered Orchidantha insularis from Hainan Island. The 2.24 Gb genome was assembled into nine pseudochromosomes, and 31 541 protein‐coding genes were annotated. Phylogenomic analysis places O. insularis within the “banana group” of Zingiberales and indicates divergence from Musaceae approximately 65 Ma, following a shared recent whole‐genome duplication (WGD). We identify significant expansions in gene families related to photosynthesis and carbon fixation, consistent with adaptation to low‐light tropical understory habitats. Our analysis uncovers the genetic basis of the carrion‐like floral scent in O. insularis by revealing complete biosynthetic pathways for dimethyl disulfide (DMDS) and indole. In parallel, the expansions of flavin‐containing monooxygenase (FMO) genes and signatures of positive selection reinforce indole metabolism, which links floral scent production to both adaptation and defense. Whole‐genome resequencing of population samples revealed high genetic differentiation and low nucleotide diversity. Demographic inference indicates severe Pleistocene bottlenecks, followed by continued population decline. Together, these results provide a genomic foundation for understanding genome evolution in early‐diverging Zingiberales and inform conservation and horticultural use.
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Claims 11
Claim · model-written summary
The 2.24 Gb genome of Orchidantha insularis was assembled into nine pseudochromosomes.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- assembled into nine pseudochromosomese1
- Value
- 2.24 Gbe1
- Setting
- Hainan Islande0
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“The 2.24 Gb genome was assembled into nine pseudochromosomes”
Claim · model-written summary
Orchidantha insularis genome annotation yielded 31 541 protein-coding genes.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- genes were annotatede2
- Value
- 31 541e1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“31 541 protein”
e2“genes were annotated”
Claim · model-written summary
Phylogenomic analysis places Orchidantha insularis within the banana group of Zingiberales.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- places O. insularis withine1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“Phylogenomic analysis places O. insularis within the”
Claim · model-written summary
Orchidantha insularis diverged from Musaceae approximately 65 Ma.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- divergence from Musaceaee1
- Value
- approximately 65 Mae1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“indicates divergence from Musaceae approximately 65 Ma”
Claim · model-written summary
A shared recent whole-genome duplication is inferred for Orchidantha insularis and Musaceae.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- shared recent whole‐genome duplicatione1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“following a shared recent whole‐genome duplication”
Claim · model-written summary
Orchidantha insularis shows significant expansions in gene families related to photosynthesis and carbon fixation.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- significant expansions in gene families related to photosynthesis and carbon fixatione1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“significant expansions in gene families related to photosynthesis and carbon fixation”
Claim · model-written summary
Complete biosynthetic pathways for dimethyl disulfide and indole were revealed in Orchidantha insularis.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Compound
- dimethyl disulfide (DMDS) and indolee1
- Outcome
- complete biosynthetic pathwayse1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“revealing complete biosynthetic pathways for dimethyl disulfide (DMDS) and indole”
Claim · model-written summary
Expansions of flavin-containing monooxygenase genes are inferred to reinforce indole metabolism in Orchidantha insularis.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Gene
- FMOe1
- Outcome
- expansions of flavin‐containing monooxygenase (FMO) genese1
- Qualifier
- reinforce indole metabolisme1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“the expansions of flavin‐containing monooxygenase (FMO) genes and signatures of positive selection reinforce indole metabolism”
Claim · model-written summary
Signatures of positive selection were found in Orchidantha insularis.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- signatures of positive selectione1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“signatures of positive selection reinforce indole metabolism”
Claim · model-written summary
Whole-genome resequencing of Orchidantha insularis populations revealed high genetic differentiation and low nucleotide diversity.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- high genetic differentiation and low nucleotide diversitye1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“revealed high genetic differentiation and low nucleotide diversity”
Claim · model-written summary
Demographic inference indicates severe Pleistocene bottlenecks followed by continued population decline in Orchidantha insularis.
- Taxon
- Orchidantha insularisOrchidantha insularise0
- Outcome
- severe Pleistocene bottlenecks, followed by continued population declinee1
Verbatim
e0“the endangered Orchidantha insularis from Hainan Island”
e1“Demographic inference indicates severe Pleistocene bottlenecks, followed by continued population decline”