Abstract：
Background:Plastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although the rapid development of high-throughput sequencing technology has led to an explosion of plastome sequences, annotation remains a significant bottleneck for plastomes. User-friendly batch annotation of multiple plastomes is an urgent need. Results:We introduce Plastid Genome Annotator (PGA), a standalone command line tool that can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plastomes. In contrast to current existing tools, PGA uses reference plastomes as the query and unannotated target plastomes as the subject to locate genes, which we refer to as the reverse query-subject BLAST search approach. PGA accurately identifies gene and intron boundaries as well as intron loss. The program outputs GenBank-formatted files as well as a log file to assist users in verifying annotations. Comparisons against other available plastome annotation tools demonstrated the high annotation accuracy of PGA, with little or no post-annotation verification necessary. Likewise, we demonstrated the flexibility of reference plastomes within PGA by annotating the plastome of Rosa roxburghii using that of Amborella trichopoda as a reference. The program, user manual and example data sets are freely available at https://github.com/quxiaojian/PGA. Conclusions:PGA facilitates rapid, accurate, and flexible batch annotation of plastomes across plants. For projects in which multiple plastomes are generated, the time savings for high-quality plastome annotation are especially significant.
journal_name
Plant Methodsjournal_title
Plant methodsauthors
Qu XJ,Moore MJ,Li DZ,Yi TSdoi
10.1186/s13007-019-0435-7subject
Has Abstractpub_date
2019-05-21 00:00:00pages
50issn
1746-4811pii
435journal_volume
15pub_type
杂志文章相关文献
Plant Methods文献大全abstract：:Plants are good sources of biologically active compounds with antimicrobial activity, including polypeptides. Antimicrobial peptides (AMPs) represent one of the main barriers of plant innate immunity to environmental stress factors and are attracting much research interest. There are some extraction methods for isolat...
journal_title：Plant methods
pub_type： 杂志文章,评审
doi：10.1186/s13007-020-00687-1
更新日期：2020-10-23 00:00:00
abstract：BACKGROUND:Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene express...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0123-9
更新日期：2016-04-26 00:00:00
abstract：: Generating and identifying transformants is essential for many studies of gene function. In Arabidopsis thaliana, a revolutionary protocol termed floral dip is now the most widely used transformation method. Although robust, it involves a number of relatively time-consuming and laborious steps, including manipulating...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-5-3
更新日期：2009-02-27 00:00:00
abstract：Background:Deep rooting is one of the most promising plant traits for improving crop yield under water-limited conditions. Most root phenotyping methods are designed for laboratory-grown plants, typically measuring very young plants not grown in soil and not allowing full development of the root system. Results:This s...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0533-6
更新日期：2019-12-09 00:00:00
abstract：BACKGROUND:Mitochondria play critical roles in plant growth, development and stress tolerance. Numerous researchers have carried out studies on the plant mitochondrial genome structure, mitochondrial metabolism and nuclear-cytoplasmic interactions. However, classical plant mitochondria extraction methods are time-consu...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00690-6
更新日期：2020-11-04 00:00:00
abstract：Background:Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bo...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0408-x
更新日期：2019-03-09 00:00:00
abstract：BACKGROUND:Striga species are noxious root hemi-parasitic weeds that debilitate cereal production in sub-Saharan Africa (SSA). Control options for Striga are limited and developing Striga resistant crop germplasm is regarded as the best and most sustainable control measure. Efforts to improve germplasm for Striga resis...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-20
更新日期：2012-06-21 00:00:00
abstract：Background:Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0362-z
更新日期：2018-10-24 00:00:00
abstract：:[This corrects the article DOI: 10.1186/s13007-017-0166-6.]. ...
journal_title：Plant methods
pub_type： 杂志文章,已发布勘误
doi：10.1186/s13007-017-0249-4
更新日期：2017-11-16 00:00:00
abstract：BACKGROUND:In silico analyses based on sequence similarities with animal channels have identified a large number of plant genes likely to encode ion channels. The attempts made to characterise such putative plant channels at the functional level have most often relied on electrophysiological analyses in classical expre...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-1-14
更新日期：2005-12-19 00:00:00
abstract：BACKGROUND:The inability to genetically transform any fern species has been a major technical barrier to unlocking fern biology. Initial attempts to overcome this limitation were based on transient transformation approaches or achieved very low efficiencies. A highly efficient method of stable transformation was recent...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-015-0080-8
更新日期：2015-07-03 00:00:00
abstract：Background:Roses are widely used as garden ornamental plants and cut flowers. Rosa chinensis cv 'Old Blush' has been used as a model genotype in rose studies due to its contribution to recurrent flowering and tea scent traits of modern roses. The deficiency of efficient genetic transformation systems is a handicap limi...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-017-0268-1
更新日期：2017-12-22 00:00:00
abstract：BACKGROUND:Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulat...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-015-0087-1
更新日期：2015-09-04 00:00:00
abstract：Background:Charcoal rot is a fungal disease that thrives in warm dry conditions and affects the yield of soybeans and other important agronomic crops worldwide. There is a need for robust, automatic and consistent early detection and quantification of disease symptoms which are important in breeding programs for the de...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0349-9
更新日期：2018-10-03 00:00:00
abstract：Background:Root is the principal part of plants to absorb water and nutrient, anchor the plant and affect yield and quality. Non-destructive detection of root traits is difficult to perform due to the hidden nature of the root. Therefore, improved methods to measure roots are necessary to support plant breeding, and op...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0414-z
更新日期：2019-03-23 00:00:00
abstract：BACKGROUND:There is considerable interest in rapid assays or screening systems for assigning gene function. However, analysis of gene function in the flowers of some species is restricted due to the difficulty of producing stably transformed transgenic plants. As a result, experimental approaches based on transient gen...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-3-1
更新日期：2007-01-08 00:00:00
abstract：BACKGROUND:Genetic studies on the molecular mechanisms of the regulation of root growth require the characterisation of a specific root phenotype to be linked with a certain genotype. Such studies using classical labour-intensive methods are severely hindered due to the technical limitations that are associated with th...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0135-5
更新日期：2016-06-24 00:00:00
abstract：Background:Plant parasitic weeds belonging to the genus Striga are a major threat for food production in Sub-Saharan Africa and Southeast Asia. The parasite's life cycle starts with the induction of seed germination by host plant-derived signals, followed by parasite attachment, infection, outgrowth, flowering, reprodu...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00602-8
更新日期：2020-05-01 00:00:00
abstract：Background:Monitoring the timing of seedling emergence and early development via high-throughput phenotyping with computer vision is a challenging topic of high interest in plant science. While most studies focus on the measurements of leaf area index or detection of specific events such as emergence, little attention ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00647-9
更新日期：2020-07-30 00:00:00
abstract：:Intact protein complexes can be separated by apparent molecular mass using a standard polyacrylamide gel electrophoresis system combining mild detergents and the dye Coomassie Blue. Referring to the blue coloured gel and the gentle method of solubilization yielding native and enzymatically active protein complexes, th...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-1-11
更新日期：2005-11-16 00:00:00
abstract：BACKGROUND:Plant metabolites are commonly functionally classified, as defense- or growth-related phytohormones, primary and specialized metabolites, and so forth. Analytical procedures for the quantifications of these metabolites are challenging because the metabolites can vary over several orders of magnitude in conce...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0130-x
更新日期：2016-05-26 00:00:00
abstract：BACKGROUND:Kinome profiling aims at the parallel analysis of kinase activities in a cell. Novel developed arrays containing consensus substrates for kinases are used to assess those kinase activities. The arrays described in this paper were already used to determine kinase activities in mammalian systems, but since sub...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-3-3
更新日期：2007-02-12 00:00:00
abstract：BACKGROUND:Artificial chromosomes (ACs) are a promising next-generation vector for genetic engineering. The most common methods for developing AC constructs are to clone and combine centromeric DNA and telomeric DNA fragments into a single large DNA construct. The AC constructs developed from such methods will contain ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-7-10
更新日期：2011-04-15 00:00:00
abstract：BACKGROUND:Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct phenotypic outputs. The identification of genes and transcriptional networks regulated by a TF often requires stable transformation and expression changes in plant cells. However, the production of stable trans...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0141-7
更新日期：2016-10-19 00:00:00
abstract：Motivation:In 2005, researchers from the French National Research Institute for Agriculture, Food and Environment (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, INRAE) started a collaboration with the French farmers' seed network Réseau Semences Paysannes (RSP) on bread wheat par...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00640-2
更新日期：2020-07-23 00:00:00
abstract：Background:Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination o...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00669-3
更新日期：2020-09-17 00:00:00
abstract：BACKGROUND:The tomato (Solanum lycopersicum L.) plant is both an economically important food crop and an ideal dicot model to investigate various physiological phenomena not possible in Arabidopsis thaliana. Due to the great diversity of tomato cultivars used by the research community, it is often difficult to reliably...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-7-18
更新日期：2011-06-29 00:00:00
abstract：: Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-6-1
更新日期：2010-01-14 00:00:00
abstract：BACKGROUND:Microsatellites are popular molecular markers in many plant species due to their stable and highly polymorphic nature. A number of analysis methods have been described but analyses of these markers are typically performed on cumbersome polyacrylamide gels or more conveniently by capillary electrophoresis on ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-4-8
更新日期：2008-05-19 00:00:00
abstract：Background:Assessing the impact of the environment on plant performance requires growing plants under controlled environmental conditions. Plant phenotypes are a product of genotype × environment (G × E), and the Enviratron at Iowa State University is a facility for testing under controlled conditions the effects of th...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0504-y
更新日期：2019-10-23 00:00:00
