A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis.
Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B....
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5578489?pdf=render |
| _version_ | 1811279277105086464 |
|---|---|
| author | Pengshan Zhao Lirong Wang Xin Zhao Guoxiong Chen Xiao-Fei Ma |
| author_facet | Pengshan Zhao Lirong Wang Xin Zhao Guoxiong Chen Xiao-Fei Ma |
| author_sort | Pengshan Zhao |
| collection | DOAJ |
| description | Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai-Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78.41% were annotated by BLASTing versus public protein databases. The B. humilis transcriptome is characterized by a high level of sequence conservation compared with its close relative, Arabidopsis thaliana. We also used reciprocal blast to identify shared orthologous genes between B. humilis and four other sequenced Brassicaceae species (i.e. A. thaliana, A. lyrata, Capsella rubella, and Thellungiella parvula). To enable precise characterization of orthologous genes, the early-diverging basal angiosperm Amborella trichopoda was also included. A total of 6,689 orthologous genes were identified before stricter criteria for the determination of e-values, amino acid hit lengths, and identity values was applied to further reduce this list. This led to a final list of 381 core orthologous genes for B. humilis; 39 out of these genes are involved in salt and osmotic stress responses and estimations of nonsynonymous/synonymous substitution ratios for this species and A. thaliana orthologs show that these genes are under purifying selection in B. humilis. Expression of six genes was detected in B. humilis seedlings under salt and osmotic stress treatments. Comparable expression patterns to their counterparts in Arabidopsis suggest that these orthologous genes are both sequence and functional conservation. The results of this study demonstrate that the environmental adaptations of B. humilis are mainly the results of preexisting genetic components. Future work will be required to characterize the expression patterns of these orthologous genes in natural populations and will provide further insights into the adaptive mechanisms underlying the wide range of B. humilis adaptations. |
| first_indexed | 2024-04-13T00:51:50Z |
| format | Article |
| id | doaj.art-2fb8a6fbf97947ba8620e011d98ea45a |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T00:51:50Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2fb8a6fbf97947ba8620e011d98ea45a2022-12-22T03:09:51ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01128e018377810.1371/journal.pone.0183778A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis.Pengshan ZhaoLirong WangXin ZhaoGuoxiong ChenXiao-Fei MaBraya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai-Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78.41% were annotated by BLASTing versus public protein databases. The B. humilis transcriptome is characterized by a high level of sequence conservation compared with its close relative, Arabidopsis thaliana. We also used reciprocal blast to identify shared orthologous genes between B. humilis and four other sequenced Brassicaceae species (i.e. A. thaliana, A. lyrata, Capsella rubella, and Thellungiella parvula). To enable precise characterization of orthologous genes, the early-diverging basal angiosperm Amborella trichopoda was also included. A total of 6,689 orthologous genes were identified before stricter criteria for the determination of e-values, amino acid hit lengths, and identity values was applied to further reduce this list. This led to a final list of 381 core orthologous genes for B. humilis; 39 out of these genes are involved in salt and osmotic stress responses and estimations of nonsynonymous/synonymous substitution ratios for this species and A. thaliana orthologs show that these genes are under purifying selection in B. humilis. Expression of six genes was detected in B. humilis seedlings under salt and osmotic stress treatments. Comparable expression patterns to their counterparts in Arabidopsis suggest that these orthologous genes are both sequence and functional conservation. The results of this study demonstrate that the environmental adaptations of B. humilis are mainly the results of preexisting genetic components. Future work will be required to characterize the expression patterns of these orthologous genes in natural populations and will provide further insights into the adaptive mechanisms underlying the wide range of B. humilis adaptations.http://europepmc.org/articles/PMC5578489?pdf=render |
| spellingShingle | Pengshan Zhao Lirong Wang Xin Zhao Guoxiong Chen Xiao-Fei Ma A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. PLoS ONE |
| title | A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. |
| title_full | A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. |
| title_fullStr | A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. |
| title_full_unstemmed | A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. |
| title_short | A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. |
| title_sort | comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in braya humilis |
| url | http://europepmc.org/articles/PMC5578489?pdf=render |
| work_keys_str_mv | AT pengshanzhao acomparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT lirongwang acomparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT xinzhao acomparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT guoxiongchen acomparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT xiaofeima acomparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT pengshanzhao comparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT lirongwang comparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT xinzhao comparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT guoxiongchen comparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis AT xiaofeima comparativetranscriptomicanalysisrevealsthecoregeneticcomponentsofsaltandosmoticstressresponsesinbrayahumilis |