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Transcriptomic profiling of the salt-stress response in the halophyte Halogeton glomeratus.

Wang J, Li B, Meng Y, Ma X, Lai Y, Si E, Yang K, Ren P, Shang X, Wang H - BMC Genomics (2015)

Bottom Line: Numerous genes that are related to ion transport, reactive oxygen species scavenging, energy metabolism, hormone-response pathways, and responses to biotic and abiotic stress appear to play a significant role in adaptation to salinity conditions in this species.The detection of expression patterns of 18 salt-induced genes by quantitative real-time polymerase chain reaction were basically consistent with their changes in transcript abundance determined by RNA sequencing.We believe that the transcriptome datasets will help elucidate the genetic basis of this species' response to a salt environment and develop stress-tolerant crops based on favorable wild genetic resources.

View Article: PubMed Central - PubMed

Affiliation: Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm Enhancement, Lanzhou, China. wang1988022020@163.com.

ABSTRACT

Background: Halogeton glomeratus (H. glomeratus) is an extreme halophyte that is widely distributed in arid regions, including foothills, the Gobi desert of northwest China, and the marginal loess of Central Asia. However, research on the salt-tolerant mechanisms and genes of this species are limited because of a lack of genomic sequences. In the present study, the transcriptome of H. glomeratus was analyzed using next-generation sequencing technology to identify genes involved in salt tolerance and better understand mechanisms of salt response in the halophyte H. glomeratus.

Results: Illumina RNA-sequencing was performed in five sequencing libraries that were prepared from samples treated with 200 mM NaCl for 6, 12, 24, and 72 h and a control sample to investigate changes in the H. glomeratus transcriptome in response to salt stress. The de novo assembly of five transcriptomes identified 50,267 transcripts. Among these transcripts, 31,496 (62.66%) were annotated, including 44 Gene Ontology (GO) terms and 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Compared with transcriptomes from the control and NaCl-treated samples, there were 2,223, 5,643, 7,510 and 10,908 genes that were differentially expressed after exposure to NaCl for 6, 12, 24, and 72 h, respectively. One hundred and eighteen salt-induced genes were common to at least two stages of salt stress, and 291 up-regulated genes were common to various stages of salt stress. Numerous genes that are related to ion transport, reactive oxygen species scavenging, energy metabolism, hormone-response pathways, and responses to biotic and abiotic stress appear to play a significant role in adaptation to salinity conditions in this species. The detection of expression patterns of 18 salt-induced genes by quantitative real-time polymerase chain reaction were basically consistent with their changes in transcript abundance determined by RNA sequencing.

Conclusions: Our findings provide a genomic sequence resource for functional genetic assignments of an extreme halophyte, H. glomeratus. We believe that the transcriptome datasets will help elucidate the genetic basis of this species' response to a salt environment and develop stress-tolerant crops based on favorable wild genetic resources.

No MeSH data available.


Related in: MedlinePlus

Length distribution at 0, 6, 12, 24, and 72 h of salt stress and all unigenes. A-F represent 0, 6, 12, 24, and 72 h and all unigenes, respectively. Values in colored square brackets indicate the range of unigene length. Unigene numbers and percentages (total number of unigenes in a certain length range) are shown next to the pie charts.
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Fig2: Length distribution at 0, 6, 12, 24, and 72 h of salt stress and all unigenes. A-F represent 0, 6, 12, 24, and 72 h and all unigenes, respectively. Values in colored square brackets indicate the range of unigene length. Unigene numbers and percentages (total number of unigenes in a certain length range) are shown next to the pie charts.

Mentions: The transcriptome sequences were assembled using the Trinity program. A total of 50,267 sequences of the five libraries were assembled, with an average of 870 bp and N50 of 1441 bp. We generated 75,832 contigs for the control sample, with an average length of 428 nt. We generated 76,045, 69,207, 73,309, and 67,563 contigs for salt-stressed samples at 6, 12, 24, and 72 h with an average length of 396, 430, 430, and 447 nt, respectively. The average N50 length was longer than 900 nt in four libraries, with the exception of the library for salt-treated samples at 6 h (785 nt). After further clustering and assembly, we obtained a total of 58,699, 60,883, 51,573, 57,557, and 53,264 unigenes with an average length of 568, 485, 566, 553, and 577 nt and N50 length of 850, 672, 826, 820, and 800 nt, respectively. The quality of these assemblies and unigenes length distribution are shown in Table 1 and Figure 2.Figure 2


Transcriptomic profiling of the salt-stress response in the halophyte Halogeton glomeratus.

Wang J, Li B, Meng Y, Ma X, Lai Y, Si E, Yang K, Ren P, Shang X, Wang H - BMC Genomics (2015)

Length distribution at 0, 6, 12, 24, and 72 h of salt stress and all unigenes. A-F represent 0, 6, 12, 24, and 72 h and all unigenes, respectively. Values in colored square brackets indicate the range of unigene length. Unigene numbers and percentages (total number of unigenes in a certain length range) are shown next to the pie charts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4363069&req=5

Fig2: Length distribution at 0, 6, 12, 24, and 72 h of salt stress and all unigenes. A-F represent 0, 6, 12, 24, and 72 h and all unigenes, respectively. Values in colored square brackets indicate the range of unigene length. Unigene numbers and percentages (total number of unigenes in a certain length range) are shown next to the pie charts.
Mentions: The transcriptome sequences were assembled using the Trinity program. A total of 50,267 sequences of the five libraries were assembled, with an average of 870 bp and N50 of 1441 bp. We generated 75,832 contigs for the control sample, with an average length of 428 nt. We generated 76,045, 69,207, 73,309, and 67,563 contigs for salt-stressed samples at 6, 12, 24, and 72 h with an average length of 396, 430, 430, and 447 nt, respectively. The average N50 length was longer than 900 nt in four libraries, with the exception of the library for salt-treated samples at 6 h (785 nt). After further clustering and assembly, we obtained a total of 58,699, 60,883, 51,573, 57,557, and 53,264 unigenes with an average length of 568, 485, 566, 553, and 577 nt and N50 length of 850, 672, 826, 820, and 800 nt, respectively. The quality of these assemblies and unigenes length distribution are shown in Table 1 and Figure 2.Figure 2

Bottom Line: Numerous genes that are related to ion transport, reactive oxygen species scavenging, energy metabolism, hormone-response pathways, and responses to biotic and abiotic stress appear to play a significant role in adaptation to salinity conditions in this species.The detection of expression patterns of 18 salt-induced genes by quantitative real-time polymerase chain reaction were basically consistent with their changes in transcript abundance determined by RNA sequencing.We believe that the transcriptome datasets will help elucidate the genetic basis of this species' response to a salt environment and develop stress-tolerant crops based on favorable wild genetic resources.

View Article: PubMed Central - PubMed

Affiliation: Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm Enhancement, Lanzhou, China. wang1988022020@163.com.

ABSTRACT

Background: Halogeton glomeratus (H. glomeratus) is an extreme halophyte that is widely distributed in arid regions, including foothills, the Gobi desert of northwest China, and the marginal loess of Central Asia. However, research on the salt-tolerant mechanisms and genes of this species are limited because of a lack of genomic sequences. In the present study, the transcriptome of H. glomeratus was analyzed using next-generation sequencing technology to identify genes involved in salt tolerance and better understand mechanisms of salt response in the halophyte H. glomeratus.

Results: Illumina RNA-sequencing was performed in five sequencing libraries that were prepared from samples treated with 200 mM NaCl for 6, 12, 24, and 72 h and a control sample to investigate changes in the H. glomeratus transcriptome in response to salt stress. The de novo assembly of five transcriptomes identified 50,267 transcripts. Among these transcripts, 31,496 (62.66%) were annotated, including 44 Gene Ontology (GO) terms and 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Compared with transcriptomes from the control and NaCl-treated samples, there were 2,223, 5,643, 7,510 and 10,908 genes that were differentially expressed after exposure to NaCl for 6, 12, 24, and 72 h, respectively. One hundred and eighteen salt-induced genes were common to at least two stages of salt stress, and 291 up-regulated genes were common to various stages of salt stress. Numerous genes that are related to ion transport, reactive oxygen species scavenging, energy metabolism, hormone-response pathways, and responses to biotic and abiotic stress appear to play a significant role in adaptation to salinity conditions in this species. The detection of expression patterns of 18 salt-induced genes by quantitative real-time polymerase chain reaction were basically consistent with their changes in transcript abundance determined by RNA sequencing.

Conclusions: Our findings provide a genomic sequence resource for functional genetic assignments of an extreme halophyte, H. glomeratus. We believe that the transcriptome datasets will help elucidate the genetic basis of this species' response to a salt environment and develop stress-tolerant crops based on favorable wild genetic resources.

No MeSH data available.


Related in: MedlinePlus