Xiaolong Ren

The complete chloroplast genome of Zelkova schneideriana (Rosales: Ulmaceae), an Endangered species endemic to China

Abstract Zelkova schneideriana Hand.-Mazz. (Ulmaceae) is an endangered species endemic to China. In this study, we reported its complete chloroplast (cp) genome based on Illumina pair-end sequencing. The whole genome was 158,999 bp long, consisting of a pair of inverted repeat (IR) regions of 26,427 bp, a large single copy (LSC) region of 87,397 bp and a small single copy (SSC) region of 18,748 bp. The cp genome contained 133 genes, including 88 protein-coding genes (80 PCG species), 37 tRNA genes (30 tRNA species), and eight rRNA genes (4 rRNA species). The overall G+C content of the whole genome was 35.6%, and the corresponding values of the LSC, SSC, and IR regions were 33.0, 28.3, and 42.4%, respectively. The maximum likelihood phylogenetic analysis of 25 selected chloroplast genomes demonstrated that Z. schneideriana was closely related to Ulmus macrocarpa and Ulmus pumila.

Characterization of the complete chloroplast genome of Lycium barbarum (Solanales: Solanaceae), a unique economic plant to China

Abstract Lycium barbarum (Solanaceae) is a unique economic plant to China. The complete chloroplast (cp)genome was sequenced and assembled by using Illumina paired-end reads data. The circular cp genome is 155,656 bp in size, including a pair of inverted repeat (IR) regions of 25,451 bp, a large single copy (LSC) region of 86,554 bp and a small single copy (SSC) region of 18,200 bp. Besides, 15 genes possess a single intron, while another three genes (clpP, rps12 and ycf3) have a couple of introns. The GC content of entire L. barbarum cp genome, LSC, SSC and IR regions are 37.8%, 35.9%, 32.3%, and 43.2%, respectively. Phylogenetic analysis based on the concatenated coding sequences of cp PCGs showed that L. barbarum and Atropa belladonna are closely related with each other within the family Solanaceae.

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

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.

Calcium oxalate degradation is involved in aerenchyma formation in Typha angustifolia leaves

Typha angustifolia L. (Typhaceae) is an emergent aquatic plant, and aerenchyma is formed through cell lysis in its leaves. The developing aerenchyma of T. angustifolia contains many CaOx crystals (raphides). Oxalate oxidase (OXO) (oxalate:oxygen oxidoreductase, EC1.2.3.4) can degrades calcium oxalate to carbon dioxide and hydrogen peroxide (H2O2). High level of H2O2 acts as a key inducer for different types of developmentally and environmentally programmed cell death (PCD) and can promote the formation of aerenchyma. Therefore, the objective of this study was to describe the relationship between aerenchyma formation and the degradation of CaOx crystals. Light and transmission electron microscopy (TEM) results showed that CaOx crystals occurred between PCD-susceptible cells in the early phase of aerenchyma formation, and those cells and CaOx crystals were degraded at aerenchyma maturation. Cytochemical localisation was used to detect H2O2, and H2O2 was found in crystal idioblasts. In addition, the oxalate content, H2O2 content and OXO activity were determined. The results showed that the concentration of oxalate was the highest in the third cavity formation stage and the H2O2 concentration was also highest at this stage. Meanwhile, the activity of OXO was also high in the third cavity formation stage. TpOXO was highly expressed during the CaOx crystal degradation period by quantitative real-time PCR analysis. These results show that the degradation of CaOx crystals is involved in the regulation of the PCD process of aerenchyma. This study will contribute to understanding the changes in CaOx crystals during the formation of aerenchyma in T. angustifolia.