Wenzhe Liu

Leaf-shape remodeling: programmed cell death in fistular leaves of Allium fistulosum.

Some species of Allium in Liliaceae have fistular leaves. The fistular lamina of Allium fistulosum undergoes a process from solid to hollow during development. The aims were to reveal the process of fistular leaf formation involved in programmed cell death (PCD) and to compare the cytological events in the execution of cell death to those in the unusual leaf perforations or plant aerenchyma formation. In this study, light and transmission electron microscopy were used to characterize the development of fistular leaves and cytological events. Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assays and gel electrophoresis were used to determine nuclear DNA cleavage during the PCD. The cavity arises in the leaf blade by degradation of specialized cells, the designated pre-cavity cells, in the center of the leaves. Nuclei of cells within the pre-cavity site become TUNEL-positive, indicating that DNA cleavage is an early event. Gel electrophoresis revealed that DNA internucleosomal cleavage occurred resulting in a characteristic DNA ladder. Ultrastructural analysis of cells at the different stages showed disrupted vacuoles, misshapen nuclei with condensed chromatin, degraded cytoplasm and organelles and emergence of secondary vacuoles. The cell walls degraded last, and residue of degraded cell walls aggregated together. These results revealed that PCD plays a critical role in the development of A. fistulosum fistular leaves. The continuous cavity in A. fistulosum leaves resemble the aerenchyma in the pith of some gramineous plants to improve gas exchange.

The complete chloroplast genome of Sinowilsonia henryi (Saxifragales: Hamamelidaceae), an endangered relict species

Sinowilsonia henryi Hemsl. (Hamamelidaceae) is a living fossil and an endangered relict species endemic to China. The complete chloroplast (cp) genome was sequenced and assembled by using Illumina paired-end reads data. The circular chloroplast genome consists of 158,741xa0bp, including a pair of inverted repeat (IR) regions of 26,233xa0bp each, a large single copy (LSC) region of 87,507xa0bp and a small single copy (SSC) region of 18,768xa0bp. The nucleotides consists of 30.5% A, 19.5% C, 18.7% G and 31.3% T. In total, the genome contained 135 genes, of which 87 are protein-coding genes (80 unique), 40 transfer RNAs (33 unique), and 8 ribosomal RNAs (4 unique). Phylogenetic analysis based on chloroplast genome sequences shows that S. henryi is closely related to Liquidambar formosana Hance.

The complete chloroplast genome of Sinojackia xylocarpa (Ericales: Styracaceae), an endangered plant species endemic to China

Sinojackia xylocarpa is an endangered plant species endemic to China. Here, we assembled its complete chloroplast genome from Illumina sequencing reads. The circular genome is 158,725xa0bp long, and contains a pair of inverted repeat regions of 26,090xa0bp each, a large single-copy region of 87,994xa0bp and a small single-copy region of 18,551xa0bp. It encodes 137 genes, including 91 protein-coding genes (82 PCG species), 38 tRNA genes (31 tRNA species) and eight rRNA genes (four rRNA species). Fifteen gene species harbor a single intron, while another two gene species have a couple of introns. The base composition is asymmetric (31.1% A, 19.0% C, 18.2% G & 31.7% T) with an overall A+T content of 62.8%. Phylogenetic analysis corroborated the traditional family-level taxonomy of the order Ericales, and suggested that S. xylocarpa is closely related to Alniphyllum eberhardtii and Bruinsmia polysperma within the family Styracaceae.

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 158,999u2009bp long, consisting of a pair of inverted repeat (IR) regions of 26,427u2009bp, a large single copy (LSC) region of 87,397u2009bp and a small single copy (SSC) region of 18,748u2009bp. 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 155,656u2009bp in size, including a pair of inverted repeat (IR) regions of 25,451u2009bp, a large single copy (LSC) region of 86,554u2009bp and a small single copy (SSC) region of 18,200u2009bp. 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.

The complete chloroplast genome of a rare species Heritiera parvifolia Merr. (Malvales: Sterculiaceae)

The precious and endangered tree, Heritiera parvifolia Merr., is an excellent landscape and ornamental species endemic to China, but its populations are now very fragmented and in decline. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of H. parvifolia by Illumina paired-end reads data. The whole genome was 160,193xa0bp, consisting of a pair of inverted repeats of 19,964xa0bp, large single copy region and a small single copy region (89,053 and 18,838xa0bp in length, respectively). The cp genome contained 130 genes, including 85 protein-coding genes, 37 trRNA genes and 8 rRNA genes. The overall GC content of the whole genome was 37.1%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between H. parvifolia and Tilia amurensis.

Characterization of the complete chloroplast genome sequence of Tapiscia sinensis (Tapisciaceae)

Tapiscia sinensis (Tapisciaceae) is an ancient and endangered tree endemic to China. Its phylogenetic position is of importance to the study of plant evolution. The complete chloroplast (cp) genome of T. sinensis was assembled using Illumina pair-end sequencing data. The circular cp genome is 161,100xa0bp long, including a pair of inverted repeat (IRs) regions of 27,407xa0bp, a large single copy (LSC) region of 87,766xa0bp and a small single copy (SSC) region of 18,520xa0bp. It encodes 131 genes, including 85 protein-coding genes (77 PCG species), 38 transfer RNA genes (30 tRNA species), and 8 transfer RNA genes (4 rRNA species). Fifteen genes harbor a single intron, while another three genes have a couple of introns. Entire T. sinensis cp genome, LSC, SSC and IR regions contain 37.2, 35.2, 31.0 and 42.4% GC, respectively. Phylogenetic analysis based on the concatenated coding sequences of cp PCGs suggests that T. sinensis is more closely related to the Sapindales than to the Malvales.

The complete chloroplast genome sequence of Fokienia hodginsii (Cupressaceae), an endangered tree

Fokienia hodginsii: is (Cupressaceae) an endangered tree species endemic to China, Vietnam and Laos. The complete chloroplast (cp) genome sequence of the F. hodginsii was determined using Illumina pair-end sequencing data. The circular genome is 127,777xa0bp long with 116 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). The genome contains 120 genes, including 83 protein-coding genes, four ribosomal RNA genes and 33 transfer RNA genes. Fifteen genes have a single intron, and two genes (rps12 and ycf3) have a couple of introns. Its cp genome does not contain canonical IRs, and the overall Au2009+u2009T content is 65.0%. Further, phylogenetic analysis suggested that F. hodginsii is closely related to species of Chamaecyparis lawsoniana.