Journal ArticleDOI
Generation and analysis of expressed sequence tags fromthe salt-tolerant eelgrass species, Zostera marina
Reads0
Chats0
TLDR
Investigation of the salt-tolerance mechanism and discover salt-Tolerant genes in Z. marina will improve understanding of the molecular mechanisms of saline tolerance in the monocotyledonous angiosperm.Abstract:
Zostera marina, a monocotyledonous angiosperm, is one of the most important seagrass species. To investigate the salt-tolerance mechanism and discover salt-tolerant genes in Z. marina, a cDNA library was constructed. Single-pass sequencing of the 5′ ends of 4 081 clones yielded 4 002 high quality expressed sequence tags (ESTs), which were assembled into 241 contigs and 1 673 singletons, representing 1 914 unigenes. The average length of the ESTs was 582 bp, with sizes ranging from 100–1 500 bp. Basic Local Alignment Search Tool (BLASTX) analysis revealed that 1 664 unigenes had significant homology to known genes in the National Center for Biotechnology Information (NCBI) non-redundant (nr) database (E-value⩽5–10). Among them, the two most abundant genes encoded metallothionein (157 ESTs) and chlorophyll a/b-binding protein (38 ESTs), accounting for 7.1% and 1.7% of the total ESTs, respectively. Using Kyoto Encyclopedia of Genes and Genomes (KEGG), 1 462 unigenes were assigned to 1 161 pathways (E-value⩽5–10). A total of 938 unigenes were assigned Gene Ontology (GO) terms based on the GO hierarchy analysis, and InterProScan searches recognized 1 003 InterPro families. Three genes for metallothionein in Z. marina that belonged to Class II was identified. Results of this study will improve understanding of the molecular mechanisms of saline tolerance in Z. marina.read more
Citations
More filters
Journal ArticleDOI
Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network
Agnieszka A. Golicz,Martin Schliep,HueyTyng Lee,HueyTyng Lee,Anthony W. D. Larkum,Rudy Dolferus,Jacqueline Batley,Chon-Kit Kenneth Chan,Chon-Kit Kenneth Chan,Gaurav Sablok,Peter J. Ralph,David Edwards +11 more
TL;DR: An aquatic life genome sequencing suggests a complete loss of genes for ethylene biosynthesis and signalling pathways in the seagrasses, Zostera muelleri andZostera marina, a new model for hormone studies.
Journal ArticleDOI
The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses
Peter John Davey,Mathieu Pernice,Gaurav Sablok,Anthony W. D. Larkum,HueyTyng Lee,Agnieszka A. Golicz,David Edwards,Rudy Dolferus,Peter J. Ralph +8 more
TL;DR: This review focuses on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology, and highlights the advances, merits and pitfalls associated with such technology.
Journal ArticleDOI
Cadmium and/or copper excess induce interdependent metal accumulation, DNA methylation, induction of metal chelators and antioxidant defences in the seagrass Zostera marina.
Maria Greco,Claudio A. Sáez,Rodrigo A. Contreras,Fernanda Rodríguez-Rojas,M. Beatrice Bitonti,Murray T. Brown +5 more
TL;DR: Under copper and/or cadmium, Z. marina was still biologically viable; certainly based, at least in part, on the induction of metal chelators, antioxidant defences and methylation/demethylation pathways of gene regulation.
Journal ArticleDOI
De Novo Assembly and Characterization of the Transcriptome of Seagrass Zostera marina Using Illumina Paired-End Sequencing
TL;DR: The transcriptome of Z. marina leaves under different environmental conditions is explored using Illumina paired-end sequencing and a large number of genes that are involved in ion transporters and channels including Na+ efflux, K+ uptake, Cl− channels, and H+ pumping are identified.
Journal ArticleDOI
Identification of Two Novel Amalgaviruses in the Common Eelgrass ( Zostera marina ) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites
TL;DR: Genome sequences of Z mAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Journal ArticleDOI
REACTIVE OXYGEN SPECIES: Metabolism, Oxidative Stress, and Signal Transduction
Klaus Apel,Heribert Hirt +1 more
TL;DR: The mechanisms of ROS generation and removal in plants during development and under biotic and abiotic stress conditions are described and the possible functions and mechanisms for ROS sensing and signaling in plants are compared with those in animals and yeast.
Journal ArticleDOI
EMBOSS: The European Molecular Biology Open Software Suite
TL;DR: The European Molecular Biology Open Software Suite is a mature package of software tools developed for the molecular biology community that includes a comprehensive set of applications for molecular sequence analysis and other tasks and integrates popular third-party software packages under a consistent interface.
Journal ArticleDOI
Reactive oxygen gene network of plants
TL;DR: In Arabidopsis, a network of at least 152 genes is involved in managing the level of ROS, and this network is highly dynamic and redundant, and encodes ROS-scavenging and ROS-producing proteins.