Abstract
Summary Spartina alterniflora is an exo‐recretohalophyte Poaceae species that is able to grow well in seashore, but the genomic basis underlying its adaptation to salt tolerance remains unknown. Here, we report a high‐quality, chromosome‐level genome assembly of S. alterniflora constructed through PacBio HiFi sequencing, combined with high‐throughput chromosome conformation capture (Hi‐C) technology and Illumina‐based transcriptomic analyses. The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb. Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA). Moreover, whole‐genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments. Comparative genomics analyses identified numerous species‐specific genes, significantly expanded genes and positively selected genes that are enriched for ‘ion transport’ and ‘response to salt stress’. RNA‐seq analysis identified several ion transporter genes including the high‐affinity K + transporters ( HKTs ), SaHKT1;2 , SaHKT1;3 and SaHKT1;8 , and high copy number of Salt Overly Sensitive ( SOS ) up‐regulated under high salt conditions, and the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant, suggesting specialized roles for S. alterniflora to adapt to saline environments. Integrated metabolomics and transcriptomics analyses revealed that salt stress activate glutathione metabolism, with differential expressions of several genes such as γ‐ECS , GSH‐S , GPX , GST and PCS in the glutathione metabolism. This study suggests several adaptive mechanisms that could contribute our understanding of evolutional basis of the halophyte.
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Claims 11
Claim · model-written summary
The chromosome-level S. alterniflora genome assembly is 1.58 Gb with contig N50 of 46.74 Mb.
- Taxon
- Spartina alterniflora
Sporobolus alterniflorust0 - Outcome
- genome assemblye0
- Value
- 1.58 Gbe0
- Qualifier
- 46.74 Mbe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb.”
t0“Spartina alterniflora”
Claim · model-written summary
S. alterniflora diverged from Zoysia japonica approximately 21.72 MYA.
- Taxon
- S. alternifloraSporobolus alternifloruse0
- Outcome
- diverged from Zoysia japonicae0
- Value
- 21.72 million years ago (MYA)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA).”
Claim · model-written summary
Whole-genome duplications appear to have expanded salt adaptation gene families and transcription factors.
- Taxon
- S. alternifloraSporobolus alternifloruse0
- Outcome
- expanded gene families and transcription factorse0
- Direction
- expandede0
- Qualifier
- whole‐genome duplication (WGD) eventse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“whole‐genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments.”
Claim · model-written summary
Species-specific genes enriched for ion transport and salt response were identified.
- Taxon
- Spartina alternifloraSporobolus alterniflorust0
- Outcome
- species‐specific genese0
- Qualifier
- enriched for ‘ion transport’ and ‘response to salt stress’e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Comparative genomics analyses identified numerous species‐specific genes, significantly expanded genes and positively selected genes that are enriched for ‘ion transport’ and ‘response to salt stress’.”
t0“Spartina alterniflora”
Claim · model-written summary
Significantly expanded genes enriched for ion transport and salt response were identified.
- Taxon
- Spartina alternifloraSporobolus alterniflorust0
- Outcome
- expanded genese0
- Direction
- expandede0
- Qualifier
- enriched for ‘ion transport’ and ‘response to salt stress’e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Comparative genomics analyses identified numerous species‐specific genes, significantly expanded genes and positively selected genes that are enriched for ‘ion transport’ and ‘response to salt stress’.”
t0“Spartina alterniflora”
Claim · model-written summary
Positively selected genes enriched for ion transport and salt response were identified.
- Taxon
- Spartina alternifloraSporobolus alterniflorust0
- Outcome
- positively selected genese0
- Qualifier
- enriched for ‘ion transport’ and ‘response to salt stress’e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Comparative genomics analyses identified numerous species‐specific genes, significantly expanded genes and positively selected genes that are enriched for ‘ion transport’ and ‘response to salt stress’.”
t0“Spartina alterniflora”
Claim · model-written summary
RNA-seq identified HKT transporter genes upregulated under high salt.
- Taxon
- Spartina alternifloraSporobolus alterniflorust0
- Treatment
- high salt conditionse0
- Gene
- SaHKT1;2e0
- Outcome
- ion transporter genese0
- Direction
- up‐regulatede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“RNA‐seq analysis identified several ion transporter genes including the high‐affinity K + transporters ( HKTs ), SaHKT1;2 , SaHKT1;3 and SaHKT1;8 , and high copy number of Salt Overly Sensitive ( SOS ) up‐regulated under high salt conditions”
t0“Spartina alterniflora”
Claim · model-written summary
High-copy SOS genes were upregulated under high salt.
- Taxon
- Spartina alternifloraSporobolus alterniflorust0
- Treatment
- high salt conditionse0
- Gene
- Salt Overly Sensitive ( SOS )e0
- Outcome
- Salt Overly Sensitive ( SOS )e0
- Direction
- up‐regulatede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“high copy number of Salt Overly Sensitive ( SOS ) up‐regulated under high salt conditions”
t0“Spartina alterniflora”
Claim · model-written summary
Overexpressing SaHKT2;4 conferred salt tolerance in Arabidopsis thaliana.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae0 - Treatment
- overexpression of SaHKT2;4e0
- Gene
- SaHKT2;4e0
- Outcome
- salt tolerancee0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant”
Claim · model-written summary
Salt stress activated glutathione metabolism.
- Taxon
- Spartina alternifloraSporobolus alterniflorust0
- Treatment
- salt stresse0
- Outcome
- glutathione metabolisme0
- Direction
- activatee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“salt stress activate glutathione metabolism, with differential expressions of several genes such as γ‐ECS , GSH‐S , GPX , GST and PCS in the glutathione metabolism.”
t0“Spartina alterniflora”
Claim · model-written summary
Salt stress altered expression of glutathione metabolism genes.
- Taxon
- Spartina alternifloraSporobolus alterniflorust0
- Treatment
- salt stresse0
- Gene
- γ‐ECSe0
- Outcome
- differential expressionse0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“salt stress activate glutathione metabolism, with differential expressions of several genes such as γ‐ECS , GSH‐S , GPX , GST and PCS in the glutathione metabolism.”
t0“Spartina alterniflora”
The same questions in other papers
salinity · molecular: metabolites · Sporobolus alterniflorus (smooth cordgrass)Positive and negative results
1 in the opposite direction
- no effect
Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.