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Background  Soil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, halophytes have attracted attention of the biologists to understand their salt adaptation mechanisms.  Spartina alterniflora  (smooth cordgrass) is a Louisiana native monocot halophyte that can withstand salinity up to double the strength of sea water. To dissect the molecular mechanisms underlying its salinity adaptation, leaf and root transcriptome of  S. alterniflora  was sequenced using 454/GS-FLX.    Results  Altogether, 770,690 high quality reads with an average length 324-bp were assembled de novo into 73,131 contigs (average 577-bp long) with 5.9X sequence coverage. Most unigenes (95 %) annotated to proteins with known functions, and had more than 90 % similarity to rice genes. About 28 % unigenes were considered specific to  S. alterniflora . Digital expression profiles revealed significant enrichment ( P  < 0.01) of transporters, vacuolar proton pump members and transcription factors under salt stress, which suggested the role of ion homeostasis and transcriptional regulation in the salinity adaptation of this grass. Also, 10,805 SSRs markers from 9457 unigenes were generated and validated through genetic diversity analysis among 13 accessions of  S. alterniflora .    Conclusions  The present study explores the transcriptome of  S. alterniflora  to understand the gene regulation under salt stress in halophytes. The sequenced transcriptome (control and salt-regulated) of  S. alterniflora  provides a platform for further gene finding studies in grasses. This study and our previously published studies suggested that  S. alterniflora  is a rich reservoir of salt tolerance genes that can be used to develop salt tolerant cereal crops, especially rice, a major food crop of global importance.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3017-3) contains supplementary material, which is available to authorized users.

bmc genomics

Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity