Genome-Wide Identification of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) Transcription Factors and Screening of Salt Stress Candidates of Rosa rugosa Thunb

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are regulators of lateral organ morphogenesis, boundary establishment, and secondary metabolism in plants. The responsive role of LBD gene family in plant abiotic stress is emerging, whereas its salt stress responsive mechanism in Rosa spp. is still unclear. The wild plant of Rosa rugosa Thunb., which exhibits strong salt tolerance to stress, is an ideal material to explore the salt-responsive LBD genes. In our study, we identified 41 RrLBD genes based on the R. rugosa genome. According to phylogenetic analysis, all RrLBD genes were categorized into Classes I and II with conserved domains and motifs. The cis-acting element prediction revealed that the promoter regions of most RrLBD genes contain defense and stress responsiveness and plant hormone response elements. Gene expression patterns under salt stress indicated that RrLBD12c, RrLBD25, RrLBD39, and RrLBD40 may be potential regulators of salt stress signaling. Our analysis provides useful information on the evolution and development of RrLBD gene family and indicates that the candidate RrLBD genes are involved in salt stress signaling, laying a foundation for the exploration of the mechanism of LBD genes in regulating abiotic stress.

De novo transcriptome analysis provides insights into formation of in vitro adventitious root from leaf explants of Arnebia euchroma

Background Adventitious root formation is considered a major developmental step during the propagation of difficult to root plants, especially in horticultural crops. Recently, adventitious roots induced through plant tissue culture methods have also been used for production of phytochemicals such as flavonoids, anthocyanins and anthraquinones. It is rather well understood which horticultural species will easily form adventitious roots, but the factors affecting this process at molecular level or regulating the induction process in in vitro conditions are far less known. The present study was conducted to identify transcripts involved in in vitro induction and formation of adventitious roots using Arnebia euchroma leaves at different time points (intact leaf (control), 3 h, 12 h, 24 h, 3 d, 7 d, 10 d and 15 d). A. euchroma is an endangered medicinal Himalayan herb whose root contains red naphthoquinone pigments. These phytoconstituents are widely used as an herbal ingredient in Asian traditional medicine as well as natural colouring agent in food and cosmetics. Results A total of 137.93 to 293.76 million raw reads were generated and assembled to 54,587 transcripts with average length of 1512.27 bps and N50 of 2193 bps, respectively. In addition, 50,107 differentially expressed genes were identified and found to be involved in plant hormone signal transduction, cell wall modification and wound induced mitogen activated protein kinase signalling. The data exhibited dominance of auxin responsive (AUXIN RESPONSE FACTOR8, IAA13, GRETCHEN HAGEN3.1) and sucrose translocation (BETA-31 FRUCTOFURANOSIDASE and MONOSACCHARIDE-SENSING protein1) genes during induction phase. In the initiation phase, the expression of LATERAL ORGAN BOUNDARIES DOMAIN16, EXPANSIN-B15, ENDOGLUCANASE25 and LEUCINE-rich repeat EXTENSION-like proteins was increased. During the expression phase, the same transcripts, with exception of LATERAL ORGAN BOUNDARIES DOMAIN16 were identified. Overall, the transcriptomic analysis revealed a similar patterns of genes, however, their expression level varied in subsequent phases of in vitro adventitious root formation in A. euchroma. Conclusion The results presented here will be helpful in understanding key regulators of in vitro adventitious root development in Arnebia species, which may be deployed in the future for phytochemical production at a commercial scale.

Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species

Background Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. Methods Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a–e, II a and II b). Results The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.

Evidence for continuity of interstitial spaces across tissue and organ boundaries in humans

Bodies have continuous reticular networks, comprising collagens, elastin, glycosaminoglycans, and other extracellular matrix components, through all tissues and organs. Fibrous coverings of nerves and blood vessels create structural continuity beyond organ boundaries. We recently validated fluid flow through human fibrous tissues, though whether these interstitial spaces are continuous through the body or discontinuous, confined within individual organs, remains unclear. Here we show evidence for continuity of interstitial spaces using two approaches. Non-biological particles (tattoo pigment, colloidal silver) were tracked within colon and skin interstitial spaces and into adjacent fascia. Hyaluronic acid, a macromolecular component of interstitial spaces, was also visualized. Both techniques demonstrate interstitial continuity within and between organs including within perineurium and vascular adventitia traversing organs and the spaces between them. We suggest that there is a body-wide network of fluid-filled interstitial spaces that has significant implications for molecular signaling, cell trafficking, and the spread of malignant and infectious disease.

Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri)

Background The lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene family has not yet been characterized for the Chinese White Pear. Results In our study, a total of 60 PbrLBDs were identified in the pear genome. The PbrLBD gene family was divided into two classes based on gene structure and phylogenetic analysis: class I (53) and class II (7). Cis-acting element analysis results suggested that PbrLBDs may participate in various biological processes, such as flavonoid biosynthetic and stress response. Synteny analysis results indicated that segmental duplication played a key role in the expansion of the PbrLBD gene family. The mean Ks and 4DTv values showed that the PbrLBD gene family had undergone only one recent whole-genome duplication event occurring at 30–45 MYA. Purifying selection was a primary force during the PbrLBD gene family evolution process. Transcriptome data analysis revealed that 10 PbrLBDs were expressed in all six examined tissues, and 73.33% of members in the PbrLBD gene family were expressed in pear sepal. qRT-PCR was conducted to verify the expression levels of 11 PbrLBDs in these six tissues. Specifically, PbrLBD20, PbrLBD35 and PbrLBD53 genes were down-regulated when anthocyanin concentrations were high, whereas PbrLBD33 was significantly up-regulated in pear when anthocyanin concentrations were high. Furthermore, PbrLBD20, one of the candidate genes related to anthocyanins was localized in the nucleus. Conclusions Our analysis provides valuable information for understanding the evolution of the PbrLBD gene family, and provides new insights into the regulation of pear pigment metabolism and lays a foundation for the future disclosure of the molecular mechanism of LBD gene regulating flavonoid metabolism.

Interstitial spaces are continuous across tissue and organ boundaries in humans

Bodies have “reticular networks” comprising collagens, elastin, glycosaminoglycans, and other extracellular matrix components, that are continuous within and around all organs. Fibrous tissue coverings of nerves and blood vessels create structural continuity beyond organ boundaries. We recently described fluid flow through such human fibrous tissues. It remains unclear whether these interstitial spaces are continuous through the body or are discontinuous, confined within individual organs. We investigated IS continuity using two approaches. Non-biological particles (tattoo pigment, colloidal silver) were tracked within colon and skin interstitial spaces and into adjacent fascia. We also exploited hyaluronic acid, a macromolecular component of interstitial spaces. Both techniques demonstrate continuity of interstitial spaces within and across organ boundaries, including within perineurium and vascular adventitia traversing organs and the spaces between them. We suggest a body-wide network of fluid-filled interstitial spaces with significant implications for molecular signaling, cell trafficking, and the spread of malignant and infectious disease.

Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus

The plant specific LATERAL ORGAN BOUNDARIES (LOB)-domain (LBD) proteins belong to a family of transcription factors that play important roles in plant growth and development, as well as in responses to various stresses. However, a comprehensive study of LBDs in Brassica napus has not yet been reported. In the present study, 126 BnLBD genes were identified in B. napus genome using bioinformatics analyses. The 126 BnLBDs were phylogenetically classified into two groups and nine subgroups. Evolutionary analysis indicated that whole genome duplication (WGD) and segmental duplication played important roles in the expansion of the BnLBD gene family. On the basis of the RNA-seq analyses, we identified BnLBD genes with tissue or developmental specific expression patterns. Through cis-acting element analysis and hormone treatment, we identified 19 BnLBD genes with putative functions in plant response to abscisic acid (ABA) treatment. This study provides a comprehensive understanding on the origin and evolutionary history of LBDs in B. napus, and will be helpful in further functional characterisation of BnLBDs.