Genome Sequence of the Plant Growth-Promoting Bacterium Enterobacter cloacae GS1

Here, we present the genome sequence of Enterobacter cloacae GS1. This strain proficiently colonizes rice roots and promotes plant growth by improving plant nutrition. Analyses of the E. cloacae GS1 genome will throw light on the genetic factors involved in root colonization, growth promotion, and ecological success of this rhizobacterium.     

A Genomic and Molecular View of Wood Formation

Wood formation is a process derived from plant secondary growth. Different from primary growth, plant secondary growth is derived from cambium meristem cells in the vascular and cork cambia and leads to the girth increase of the plant trunk. In the secondary growth process, plants convert most of photosynthesized products into various biopolymers for use in the formation of woody tissues. This article summarizes the new developments of genomic and genetic characterization of wood formation in herbaceous model plant and tree plant systems. Genomic studies have categorized a collection of the genes for which expression is associated with secondary growth. During wood formation, the expression of many genes is regulated in a stage-specific manner. The function of many genes involved in wood biosyntheses and xylem differentiation has been characterized. Although great progress has been achieved in the molecular and genomic understanding of plant secondary growth in recent years, the profound genetic mechanisms underlying this plant development remain to be investigated. Completion of the first tree genome sequence (Populus genome) provides a valuable genomic resource for characterization of plant secondary growth.     

Complete genome sequence of Serratia plymuthica strain AS12

A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens".     

Mechanisms and rates of genome expansion and contraction in flowering plants

Plant genomes are exceptional for their great variation in genome size, an outcome derived primarily from their frequent polyploid origins and from the amplification of retrotransposons. Although most studies of plant genome size variation have focused on developmental or physiological effects of nuclear DNA content that might influence plant fitness, more recent studies have begun to investigate possible mechanisms for plant genome expansion and contraction. Analyses of relatively neutral genome components, like transposable elements, have been particularly fruitful, largely due to the enormous growth in genomic sequence information from many different plant species. Current data suggest that unequal recombination can slow the growth in genome size caused by retrotransposon amplification, but that illegitimate recombination and other deletion processes may be primarily responsible for the removal of non-essential DNA from small genome plants.     

Complete genome sequence of plant growth promoting Pseudomonas aeruginosa AJ D 2 an isolate from monocropic cotton rhizosphere

A plant growth promoting Pseudomonas aeruginosa AJD 2 was isolated from monocropic cotton rhizosphere of Maharashtra state, India. The strain was identified as per physiological, biochemical and 16S rRNA gene sequencing (Accession number MG234531). The strain possess multiple functional plant growth promoting traits and antifungal activity. The genome was extracted, purified and library of avg.515 bp was prepared and sequenced by over Illumina platform. The sequenced genome was studied by using CLC workbench and NCBI pipeline using Pseudomonas aeruginosa PAO1 and Pseudomonas aeruginosa YL84 as reference assembler. The size of the genome is 6.1 Mb with 5802 genes within it. The study over strain may give an insight into its plant growth promotion mechanism.     

Genome sequence of the diazotrophic Gram-positive rhizobacterium Paenibacillus riograndensis SBR5(T)

Paenibacillus riograndensis SBR5(T), a nitrogen-fixing Gram-positive rhizobacterium isolated from a wheat field in the south of Brazil, has a great potential for agricultural applications due to its plant growth promotion effects. Here we present the draft genome sequence of P. riograndensis SBR5(T). Its 7.37-Mb genome encodes determinants of the diazotrophic lifestyle and plant growth promotion, such as nitrogen fixation, antibiotic resistance, nitrate utilization, and iron uptake.     

Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9

Serratia plymuthica are plant-associated, plant beneficial species belonging to the family Enterobacteriaceae. The members of the genus Serratia are ubiquitous in nature and their life style varies from endophytic to free-living. S. plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The genome of S. plymuthica AS9 comprises a 5,442,880 bp long circular chromosome that consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI Community Sequencing Program (CSP2010).     

Draft genome sequence of Pantoea ananatis B1-9, a nonpathogenic plant growth-promoting bacterium

Pantoea ananatis B1-9 is an endophytic Gram-negative rhizobacterium that was isolated for its ability to promote plant growth and improve crop yield in the field. Here we report the draft genome sequence of P. ananatis B1-9. Comparison of this sequence to the sequenced genome of a plant-pathogenic P. ananatis strain, LMG20103, indicated that the pathogenesis-related genes were absent, but a subset of gene functions that may be related to its plant growth promotion were present.     

Complete Genome Sequence of the Endophytic Bacterium Burkholderia sp. Strain KJ006

Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of Burkholderia sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.     

如何检索国外植物生物学相关网站

植物生长与发育、植物细胞信号和基因调控、植物基因组研究等三个领域是当前植物生物学研究的热点。我们介绍了与这三个领域有关的国外主要网站,以期对植物生物学研究者有所帮助。     

植物线粒体基因的表达及控制的生命现象

线粒体控制的生命活动多种多样,决定植物的生长发育,本文对线粒体基因组特点,表达及其控制的生命现象等有内容作一总结。     

Engineering Resistance Against Viruses in Field Crops Using CRISPR- Cas9

Food security is threatened by various biotic stresses that affect the growth and production of agricultural crops. Viral diseases have become a serious concern for crop plants as they incur huge yield losses. The enhancement of host resistance against plant viruses is a priority for the effective management of plant viral diseases. However, in the present context of the climate change scenario, plant viruses are rapidly evolving, resulting in the loss of the host resistance mechanism. Advances in genome editing techniques, such as CRISPR-Cas9 [clustered regularly interspaced palindromic repeats-CRISPR-associated 9], have been recognized as promising tools for the development of plant virus resistance. CRISPR-Cas9 genome editing tool is widely preferred due to high target specificity, simplicity, efficiency, and reproducibility. CRISPR-Cas9 based virus resistance in plants has been successfully achieved by gene targeting and cleaving the viral genome or altering the plant genome to enhance plant innate immunity. In this article, we have described the CRISPR-Cas9 system, mechanism of plant immunity against viruses and highlighted the use of the CRISPR-Cas9 system to engineer virus resistance in plants. We also discussed prospects and challenges on the use of CRISPR-Cas9-mediated plant virus resistance in crop improvement.     

Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1

We report the complete sequence of the 5.7-Mbp genome of Pseudomonas putida BIRD-1, a metabolically versatile plant growth-promoting rhizobacterium that is highly tolerant to desiccation and capable of solubilizing inorganic phosphate and iron and of synthesizing phytohormones that stimulate seed germination and plant growth.     

Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain 916

Bacillus sp. strain 916, isolated from the soil, showed strong activity against Rhizoctonia solani. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 916. Its 3.9-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.     

Complete genome sequence of a beneficial plant root-associated bacterium, Pseudomonas brassicacearum

To shed light on the genetic equipment of the beneficial plant-associated bacterium Pseudomonas brassicacearum, we sequenced the whole genome of the strain NFM421. Its genome consists of one chromosome equipped with a repertoire of factors beneficial for plant growth. In addition, a complete type III secretion system and two complete type VI secretion systems were identified. We report here the first genome sequence of this species.     

一株连香树根际促生细菌LWK2的分离鉴定及其全基因组序列分析

【背景】植物根际促生细菌是一类位于植物根际并能对植物生长产生促进作用的有益菌,在微生物肥料领域具有重要的应用价值。【目的】对濒危植物连香树根际的植物根际促生细菌进行分离筛选和连香树接种效应评价,挑选对连香树生长促进作用最为显著的菌种进行促生特性分析、菌种鉴定及全基因组序列测定与促生相关基因分析。【方法】利用相应筛选培养基对连香树根际土壤中解有机磷、溶无机磷和解钾细菌进行分离筛选,通过根际接种验证各菌株对连香树实生苗的促生能力。从中选取促生作用最为显著的细菌,进行解钾能力、产吲哚乙酸(indole-3-acetic acid,IAA)和1-氨基环丙烷-1-羧酸(1-aminocyclopropane-1-carboxylate,ACC)脱氨酶能力测定。利用菌体形态观察、16S rRNA基因序列分析及全基因组序列的平均核苷酸一致性比对进行菌种鉴定。最后利用基因组功能注释和比较基因组学分析对该菌株中的植物促生及重金属抗性相关基因进行解析。【结果】从连香树根际土壤中共筛选得到3株解有机磷细菌、2株溶无机磷细菌和2株解钾细菌,其中解钾细菌LWK2对连香树实生苗的生长促进作用最为显著。该菌株能够产...     

Draft Genome Sequence of the Endophytic Bacterium Enterobacter spp. MR1, Isolated from Drought Tolerant Plant (Butea monosperma)

Enterobacter sp. MR1 an endophytic plant growth promoting bacterium was isolated from the roots of Butea monosperma, a drought tolerant plant. Genome sequencing of Enterobacter spp. MR1 was carried out in Ion Torrent (PGM), Next Generation Sequencer. The data obtained revealed 640 contigs with genome size of 4.58 Mb and G+C content of 52.8 %. This bacterium may contain genes responsible for inducing drought tolerance in plant, including genes for phosphate solubilization, growth hormones and other useful genes for plant growth.     

Plant mitochondrial recombination surveillance requires unusual RecA and MutS homologs

For >20 years, the enigmatic behavior of plant mitochondrial genomes has been well described but not well understood. Chimeric genes appear, and occasionally are differentially replicated or expressed, with significant effects on plant phenotype, most notably on male fertility, yet the mechanisms of DNA replication, chimera formation, and recombination have remained elusive. Using mutations in two important genes of mitochondrial DNA metabolism, we have observed reproducible asymmetric recombination events occurring at specific locations in the mitochondrial genome. Based on these experiments and existing models of double-strand break repair, we propose a model for plant mitochondrial DNA replication, chimeric gene formation, and the illegitimate recombination events that lead to stoichiometric changes. We also address the physiological and developmental effects of aberrant events in mitochondrial genome maintenance, showing that mitochondrial genome rearrangements, when controlled, influence plant reproduction, but when uncontrolled, lead to aberrant growth phenotypes and dramatic reduction of the cell cycle.     

The effect of genome size on detailed species traits within closely related species of the same habitat

In spite of the large number of studies on genome size, studies comparing genome size and growth‐related traits across a wider range of species from the same habitat, taking into account species phylogeny, are largely missing. I estimated the relationship between genome size and different seed and seedling traits in perennial herbs occurring in dry calcareous grasslands in northern Bohemia, Czech Republic. There was no relationship between genome size and plant traits in simple regression analyses, but several strong relationships emerged in analyses based on pairwise phylogenetically independent contrasts. There was a significant relationship between monoploid genome size and production of above‐ground biomass, seedling establishment success and seed weight and between holoploid genome size and seed dormancy. Because the results are based on phylogenetically independent contrasts over a range of species from the same type of habitat, they allow me to conclude that these patterns were not because of species group or habitat type, but really show a correlation with genome size. In contrast to previous studies, I found a higher number of relationships with monoploid than with holoploid genome size. This may be because the traits observed in this study are directly related to plant growth and thus to life‐cycle time, which is determined by monoploid genome size. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 290–298.     

Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42

Bacillus amyloliquefaciens FZB42 is a Gram-positive, plant-associated bacterium, which stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. Its 3,918-kb genome, containing an estimated 3,693 protein-coding sequences, lacks extended phage insertions, which occur ubiquitously in the closely related Bacillus subtilis 168 genome. The B. amyloliquefaciens FZB42 genome reveals an unexpected potential to produce secondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5% of the genome is devoted to synthesizing antibiotics and siderophores by pathways not involving ribosomes. Besides five gene clusters, known from B. subtilis to mediate nonribosomal synthesis of secondary metabolites, we identified four giant gene clusters absent in B. subtilis 168. The pks2 gene cluster encodes the components to synthesize the macrolactin core skeleton.