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Comparative transcriptome analysis of the Asteraceae halophyte Karelinia caspica under salt stress.
BMC Res Notes. 2014 Dec 17; 7:927.BR

Abstract

BACKGROUND

Much attention has been given to the potential of halophytes as sources of tolerance traits for introduction into cereals. However, a great deal remains unknown about the diverse mechanisms employed by halophytes to cope with salinity. To characterize salt tolerance mechanisms underlying Karelinia caspica, an Asteraceae halophyte, we performed Large-scale transcriptomic analysis using a high-throughput Illumina sequencing platform. Comparative gene expression analysis was performed to correlate the effects of salt stress and ABA regulation at the molecular level.

RESULTS

Total sequence reads generated by pyrosequencing were assembled into 287,185 non-redundant transcripts with an average length of 652 bp. Using the BLAST function in the Swiss-Prot, NCBI nr, GO, KEGG, and KOG databases, a total of 216,416 coding sequences associated with known proteins were annotated. Among these, 35,533 unigenes were classified into 69 gene ontology categories, and 18,378 unigenes were classified into 202 known pathways. Based on the fold changes observed when comparing the salt stress and control samples, 60,127 unigenes were differentially expressed, with 38,122 and 22,005 up- and down-regulated, respectively. Several of the differentially expressed genes are known to be involved in the signaling pathway of the plant hormone ABA, including ABA metabolism, transport, and sensing as well as the ABA signaling cascade.

CONCLUSIONS

Transcriptome profiling of K. caspica contribute to a comprehensive understanding of K. caspica at the molecular level. Moreover, the global survey of differentially expressed genes in this species under salt stress and analyses of the effects of salt stress and ABA regulation will contribute to the identification and characterization of genes and molecular mechanisms underlying salt stress responses in Asteraceae plants.

Authors+Show Affiliations

Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 14 Sheng li Road, Urumqi 830046, China. xia.zhangxjkt@gmail.com.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25515859

Citation

Zhang, Xia, et al. "Comparative Transcriptome Analysis of the Asteraceae Halophyte Karelinia Caspica Under Salt Stress." BMC Research Notes, vol. 7, 2014, p. 927.
Zhang X, Liao M, Chang D, et al. Comparative transcriptome analysis of the Asteraceae halophyte Karelinia caspica under salt stress. BMC Res Notes. 2014;7:927.
Zhang, X., Liao, M., Chang, D., & Zhang, F. (2014). Comparative transcriptome analysis of the Asteraceae halophyte Karelinia caspica under salt stress. BMC Research Notes, 7, 927. https://doi.org/10.1186/1756-0500-7-927
Zhang X, et al. Comparative Transcriptome Analysis of the Asteraceae Halophyte Karelinia Caspica Under Salt Stress. BMC Res Notes. 2014 Dec 17;7:927. PubMed PMID: 25515859.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparative transcriptome analysis of the Asteraceae halophyte Karelinia caspica under salt stress. AU - Zhang,Xia, AU - Liao,Maoseng, AU - Chang,Dan, AU - Zhang,Fuchun, Y1 - 2014/12/17/ PY - 2013/11/04/received PY - 2014/12/11/accepted PY - 2014/12/18/entrez PY - 2014/12/18/pubmed PY - 2015/9/12/medline SP - 927 EP - 927 JF - BMC research notes JO - BMC Res Notes VL - 7 N2 - BACKGROUND: Much attention has been given to the potential of halophytes as sources of tolerance traits for introduction into cereals. However, a great deal remains unknown about the diverse mechanisms employed by halophytes to cope with salinity. To characterize salt tolerance mechanisms underlying Karelinia caspica, an Asteraceae halophyte, we performed Large-scale transcriptomic analysis using a high-throughput Illumina sequencing platform. Comparative gene expression analysis was performed to correlate the effects of salt stress and ABA regulation at the molecular level. RESULTS: Total sequence reads generated by pyrosequencing were assembled into 287,185 non-redundant transcripts with an average length of 652 bp. Using the BLAST function in the Swiss-Prot, NCBI nr, GO, KEGG, and KOG databases, a total of 216,416 coding sequences associated with known proteins were annotated. Among these, 35,533 unigenes were classified into 69 gene ontology categories, and 18,378 unigenes were classified into 202 known pathways. Based on the fold changes observed when comparing the salt stress and control samples, 60,127 unigenes were differentially expressed, with 38,122 and 22,005 up- and down-regulated, respectively. Several of the differentially expressed genes are known to be involved in the signaling pathway of the plant hormone ABA, including ABA metabolism, transport, and sensing as well as the ABA signaling cascade. CONCLUSIONS: Transcriptome profiling of K. caspica contribute to a comprehensive understanding of K. caspica at the molecular level. Moreover, the global survey of differentially expressed genes in this species under salt stress and analyses of the effects of salt stress and ABA regulation will contribute to the identification and characterization of genes and molecular mechanisms underlying salt stress responses in Asteraceae plants. SN - 1756-0500 UR - https://www.unboundmedicine.com/medline/citation/25515859/Comparative_transcriptome_analysis_of_the_Asteraceae_halophyte_Karelinia_caspica_under_salt_stress_ DB - PRIME DP - Unbound Medicine ER -