Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq

Abstract

Carex rigescens (Franch.) V. Krecz is a wild turfgrass perennial species in the Carex genus that is widely distributed in salinised areas of northern China. To investigate genome-wide salt-response gene networks in C. rigescens, transcriptome analysis using high-throughput RNA sequencing on C. rigescens exposed to a 0.4% salt treatment (Cr_Salt) was compared to a non-salt control (Cr_Ctrl). In total, 57 742 546 and 47 063 488 clean reads were obtained from the Cr_Ctrl and Cr_Salt treatments, respectively. Additionally, 21 954 unigenes were found and annotated using multiple databases. Among these unigenes, 34 were found to respond to salt stress at a statistically significant level with 6 genes up-regulated and 28 downregulated. Specifically, genes encoding an EF-hand domain, ZFP and AP2 were responsive to salt stress, highlighting their roles in future research regarding salt tolerance in C. rigescens and other plants. According to our quantitative RT-PCR results, the expression pattern of all detected differentially expressed genes were consistent with the RNA-seq results. Furthermore, we identified 11 643 simple sequence repeats (SSRs) from the unigenes. A total of 144 amplified successfully in the C. rigescens cultivar Lüping 1, and 69 of them reflected polymorphisms between the two genotypes tested. This is the first genome-wide transcriptome study of C. rigescens in both salt-responsive gene investigation and SSR marker exploration. Our results provide further insights into genome annotation, novel gene discovery, molecular breeding and comparative genomics in C. rigescens and related grass species.

Characterization of Dendrolimus houi Lajonquiere (Lepidoptera: Lasiocampidae) Transcriptome across All Life Stages

“…Technically, molecular marker is an important method for population genetics research [50,51]. In this study, 4138 SSR genes and 114,977 SNP loci were identified from the transcriptome of D. houi, mono-nucleotide repeat is the main type of SSR, accounting for the largest proportion, the trinonucleotide repeat was the most common type, which is similar to results of some previous research on Epacromius coerulipes [52], Bactrocera dorsalis [53].…”

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome

“…Carex , one of the largest genus in Cyperaceae, contains more than 2000 species and plays important roles in turfgrass and forage production as well as in ecological conservation [1]. However, our current knowledge on Carex species transcriptomes is mainly based on gene expression analysis of Carex rigescens using NGS technologies [3]. Moreover, the Carex.…”

“…The wide application of transcriptome sequencing has promoted plant breeding and revealed gene regulation networks in plants [2]. However, few studies have focused on the transcriptome of Carex L., with previous studies being limited to physiological investigation and stress-resistance evaluation [3, 4]. Consequently, progress in the study of the transcriptome of the genus lags far behind.…”

Carex muskingumensis and Osmotic Stress: Identification of Reference Genes for Transcriptional Profiling by RT-qPCR

“…Since no sequences for C. muskingumensis were available, Carex rigescens sequences deposited in GeneBank or SRA database (Sequence Read Archive accession No. SRX2755644) [ 27 ] were used for primer designing. Arabidopsis thaliana and Zea mays nucleotide sequences were used as query sequences for performed BLASTN search.…”

“…The information on sedges’ molecular responses to osmotic stress and their adaptation mechanisms is limited [ 27 , 28 , 29 ]. To address this issue, our study aims at identifying best RGs for C. muskingumensis under salt and drought stress.…”