Abstract
The genomic shock of whole-genome duplication (WGD) and hybridization introduces great variation into transcriptomes, for both coding and noncoding genes. An altered transcriptome provides a molecular basis for improving adaptation during the evolution of new species. The allotetraploid cotton, together with the putative diploid ancestor species compose a fine model for study the rapid gene neofunctionalization over the genome shock. Here we report on Drought-Associated Non-coding gene 1 (DAN1), a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution. DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm. Chromatin isolation by RNA purification profiling and electrophoretic mobility shift assay analysis demonstrated that GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences. The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation. As a result, GhDAN1-silenced plants exhibit improved tolerance to drought stress. This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1. The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process.
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Claims 8
Claim · model-written summary
DAN1 is a drought-responsive lincRNA in allotetraploid upland cotton.
Verbatim
e0“DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm”
Claim · model-written summary
DAN1 is predominantly expressed in the nucleoplasm of upland cotton.
Verbatim
e0“DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm”
Claim · model-written summary
The DAN1 lincRNA arose from the cotton progenitor A-diploid genome after hybridization and WGD events.
- Taxon
- cotton
Gossypium hirsutume1 - Outcome
- arose from the cotton progenitor A-diploid genome after hybridization and WGD eventse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution”
Claim · model-written summary
GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences.
Verbatim
e0“DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm”
e2“GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences”
Claim · model-written summary
Suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways.
- Taxon
- upland cottone0
- Treatment
- suppression of GhDAN1e3
- Gene
- GhDAN1e3
- Outcome
- genes with AAAG motifs in auxin-response pathwayse3
- Qualifier
- mainlye3
Not reportedDirection
Verbatim
e0“DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm”
e3“The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation”
Claim · model-written summary
GhDAN1-silenced plants exhibit improved tolerance to drought stress.
- Taxon
- upland cottone0
- Treatment
- GhDAN1-silencede4
- Gene
- GhDAN1e4
- Outcome
- tolerance to drought stresse4
- Direction
- improvede4
Not reportedComparator
Verbatim
e0“DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm”
e4“GhDAN1-silenced plants exhibit improved tolerance to drought stress”
Claim · model-written summary
The GhDAN1-silenced phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has undetectable DAN1 expression.
Verbatim
e5“This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1”
Claim · model-written summary
Genomic shock of interspecific hybridization and WGD is suggested to have stimulated neofunctionalization of non-coding genes in cotton.
- Taxon
- cottonGossypium hirsutume6
- Gene
- DAN1e6
- Outcome
- neofunctionalization of non-coding genese6
- Qualifier
- the genomic shock of interspecific hybridization and WGDe6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e6“The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process”