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

Abstract

BackgroundSoil 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.ResultsAltogether, 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.ConclusionsThe 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 materialThe online version of this article (doi:10.1186/s12864-016-3017-3) contains supplementary material, which is available to authorized users.

Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands

“…offer multiple snapshots into the leaf transcriptomics that investigate how salt glands contribute to salt tolerance (Baisakh et al, 2008; Ferreira de Carvalho et al, 2013; Bedre et al, 2016). Spartina is among the few recretohalophytes where both RNASeq and microRNASeq profiles are available (Qin et al, 2015; Zandkarimi et al, 2015).…”

The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

“…We used PacBio SMRT sequencing to obtain full-length reference transcripts of high-confidence in Spartina to avoid potential bias attributed to its complex aneu-hexaploid genome (2n = 6x = 62) (Bedre, Mangu, Srivastava, Sanchez, & Baisakh, 2016). An overview of the experimental procedure is illustrated in Fig.…”

“…( c ) Comparison of transcripts identified from RNA-seq and PacBio data. Contigs from de novo assembly of RNA-seq data (Bedre et al ., 2016) were mapped to PacBio full-length transcripts (FLs), and vice versa. nContigs: the number of de novo -assembled contigs from RNA-seq data; nQ: the number of contigs mapped to PacBio FLs; pQ: the percentage of contigs mapped to FLs; nS: the number of FLs mapped to contigs; pS: the percentage of FLs mapped to contigs.…”

An actin‐depolymerizing factor from the halophyte smooth cordgrass, Spartina alterniflora (SaADF2), is superior to its rice homolog (OsADF2) in conferring drought and salt tolerance when constitutively overexpressed in rice

“…Downstream sequence manipulations, such as filtering, mapping, assembly, differential gene expression, GO and KEGG analyses, were performed following Bedre et al (2016).…”