De novo transcriptomic analysis to identify differentially expressed genes during the process of aerenchyma formation in Typha angustifolia leaves

Abstract

Lysigenous aerenchyma is formed through programmed cell death (PCD) in Typha angustifolia leaves. However, the genome and transcriptome data for this species are unknown. To further elucidate the molecular basis of PCD during aerenchyma formation in T. angustifolia leaves, transcriptomic analysis of T. angustifolia leaves was performed using Illumina sequencing technology, revealing 73,821 unigenes that were produced by assembly of the reads in T1, T2 and T3 samples. The important pathways, such as programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness were regulated by these unigenes. 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylate oxidase (ACO) were highly up-regulated as key enzymes for ethylene synthesis, along with respiratory burst oxidase homolog (RBOH), metallothionein, calmodulin-like protein (CML), and polygalacturonase (PG), may collectively explain the PCD involved in T. angustifolia aerenchyma formation. We hypothesize that fermentation, metabolism and glycolysis generate ATP for PCD. We searched the 73,821 unigenes against protein databases, and 24,712 were annotated. Based on sequence homology, 16,012 of the 73,821 annotated unigenes were assigned to one or more Gene Ontology (GO) terms. Meanwhile, a total of 9537 unigenes were assigned to 126 pathways in the KEGG database. In summary, this investigation provides important guidelines for exploring the molecular mechanisms of aerenchyma formation in aquatic plants.

Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

“…Differential expression analysis of the three stages in MF and HF was performed using DESeq [116]. DESeq2 v1.4.5 was used for differential gene expression analysis, and a p -value could be assigned to each gene and adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate.…”

“…Primer sequences were designed using Primer premier 5.0, and Primer sequences and β - actin (as an internal control to normalize the expression levels of genes) sequence of internal reference gene are listed in Additional file 1. RNA was extracted from T. sinensis of three developmental stages, and RNA extraction, cDNA synthesis, and Real-time PCR method as described in related references [116, 123].…”

Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

“…Since the WL-S accession revealed up-regulation of this gene after the second treatment (2xH), it could suggest that waterlogging acted as a priming factor in acquiring tolerance to waterlogging stress in the WL-S accession. Calmodulin-like proteins (CMLs) are sensors of Ca 2+ and take part in calcium signaling [68]. It has been reported that CMLs may be involved in aerenchyma formation, allowing plants to perform gas exchange between roots and shoots [69].…”

RNA-Seq analysis reveals potential regulators of programmed cell death and leaf remodelling in lace plant (Aponogeton madagascariensis)

“…RNA-Seq analysis of separated embryonal mass and suspensor cells of Picea abies has shown that a spruce homolog of bax inhibitor-1 transcript is upregulated in early PCD suspensor cells and plays a role in regulating vacuolar cell death in suspensor cells [ 19 ]. Moreover, RNA-Seq analysis of early and late cavern forming leaf aerenchyma cells of Typha angustifolia revealed expansins, calmodulin-like proteins and pectinases transcripts that were directly related to lysigenous aerenchyma induction [ 20 ].…”