Abstract
The origin and evolutionary dynamics of long non-coding RNAs (lncRNAs) represent a pivotal frontier in plant functional genomics. Here, we investigated pseudo-GhFAD2-1 ( pGhFAD2-1 ), a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum , delineating its evolutionary origin and structural dynamics through a comprehensive cross-genomic comparative strategy. Homologous sequence identification, phylogenetic reconstruction, and molecular evolutionary analyses were conducted across 27 Gossypium species representing the A, B, D, E, F, G, K, and AD genomes. Our findings reveal that pGhFAD2–1 originated from a tandem duplication event of GhFAD2-1D in the D-genome ancestor approximately 5 million years ago (MYA). This duplicated locus was subsequently disrupted by a 1,221-bp exogenous sequence insertion, which abolished its protein-coding capacity and catalyzed the emergence of this novel lncRNA transcript. Subjected to strong purifying selection, this reorganized locus retained its core functional domain and exhibited high-fidelity inheritance (sequence identity>85%) across D-genome diploids and AD-genome allotetraploids. Conversely, only fragmented remnants or complete deletions of this locus were detected in non-D genome Gossypium species. This study systematically characterizes the evolutionary trajectory and subgenomic conservation of pGhFAD2-1 , elucidating its adaptive significance as a D-lineage-specific lncRNA. These findings provide novel insights into how lineage-specific structural variations rewire epigenetic regulatory networks to drive adaptive diversification in allopolyploid crops, establishing an evolution-informed molecular target for the synergistic genetic improvement of cotton fiber and seed oil traits.
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Claims 8
Claim · model-written summary
pGhFAD2-1 originated from a tandem duplication of GhFAD2-1D in the D-genome ancestor about 5 million years ago.
- Taxon
- Gossypium hirsutum
Gossypium hirsutume0 - Outcome
- originatede1
- Value
- approximately 5 million years agoe1
- Qualifier
- tandem duplication event of GhFAD2-1De1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum”
e1“originated from a tandem duplication event of GhFAD2-1D in the D-genome ancestor approximately 5 million years ago (MYA)”
Claim · model-written summary
A 1,221-bp exogenous sequence insertion disrupted the duplicated locus and abolished its protein-coding capacity.
- Taxon
- Gossypium hirsutumGossypium hirsutume0
- Outcome
- protein-coding capacitye2
- Value
- 1,221-bpe2
- Qualifier
- exogenous sequence insertione2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum”
e2“disrupted by a 1,221-bp exogenous sequence insertion, which abolished its protein-coding capacity”
Claim · model-written summary
The reorganized locus showed high-fidelity inheritance (sequence identity above 85%) across D-genome diploids and AD-genome allotetraploids.
- Taxon
- Gossypium hirsutumGossypium hirsutume0
- Material
- D-genome diploids and AD-genome allotetraploidse3
- Outcome
- sequence identitye3
- Value
- >85%e3
- Qualifier
- high-fidelity inheritancee3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum”
e3“exhibited high-fidelity inheritance (sequence identity>85%) across D-genome diploids and AD-genome allotetraploids”
Claim · model-written summary
Under strong purifying selection the reorganized locus retained its core functional domain.
- Taxon
- Gossypium hirsutumGossypium hirsutume0
- Outcome
- core functional domaine6
- Qualifier
- strong purifying selectione6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum”
e6“Subjected to strong purifying selection, this reorganized locus retained its core functional domain”
Claim · model-written summary
The locus was detected only as fragmented remnants or complete deletions in non-D genome Gossypium species.
- Outcome
- fragmented remnants or complete deletionse4
GossypiumOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“Conversely, only fragmented remnants or complete deletions of this locus were detected in non-D genome Gossypium species”
Claim · model-written summary
The authors interpret pGhFAD2-1 as an adaptive D-lineage-specific lncRNA.
- Taxon
- Gossypium hirsutumGossypium hirsutume0
- Outcome
- adaptive significancee5
- Qualifier
- D-lineage-specific lncRNAe5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum”
e5“elucidating its adaptive significance as a D-lineage-specific lncRNA”
Claim · model-written summary
The authors propose pGhFAD2-1 as an evolution-informed molecular target for genetic improvement of cotton fiber and seed oil traits.
- Taxon
- cottonGossypium hirsutume7
- Outcome
- synergistic genetic improvement of cotton fiber and seed oil traitse7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“establishing an evolution-informed molecular target for the synergistic genetic improvement of cotton fiber and seed oil traits”
Claim · model-written summary
The authors suggest that lineage-specific structural variation rewires epigenetic networks to drive adaptive diversification in Gossypium.
- Taxon
- Gossypium hirsutumGossypium hirsutume0
- Outcome
- adaptive diversificatione7
- Qualifier
- lineage-specific structural variations rewire epigenetic regulatory networkse7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum”
e7“These findings provide novel insights into how lineage-specific structural variations rewire epigenetic regulatory networks to drive adaptive diversification in allopolyploid crops”