Abstract：
:The commercial release of third-generation sequencing technologies (TGSTs), giving long and ultra-long sequencing reads, has stimulated the development of new tools for assembling highly contiguous genome sequences with unprecedented accuracy across complex repeat regions. We survey here a wide range of emerging sequencing platforms and analytical tools for de novo assembly, provide background information for each of their steps, and discuss the spectrum of available options. Our decision tree recommends workflows for the generation of a high-quality genome assembly when used in combination with the specific needs and resources of a project.
journal_name
Trends Plant Scijournal_title
Trends in plant scienceauthors
Jung H,Winefield C,Bombarely A,Prentis P,Waterhouse Pdoi
10.1016/j.tplants.2019.05.003subject
Has Abstractpub_date
2019-08-01 00:00:00pages
700-724issue
8eissn
1360-1385issn
1878-4372pii
S1360-1385(19)30121-9journal_volume
24pub_type
杂志文章,评审abstract：:More than half of the flowering plants have a sophisticated mechanism for self-pollen rejection, named self-incompatibility (SI). In Brassicaceae, recognition specificity is achieved by the interaction of the stigmatic S-RECEPTOR KINASE (SRK) and its ligand S-LOCUS CYSTEINE-RICH PROTEIN (SCR). Recent years have seen s...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2010.04.010
更新日期：2010-07-01 00:00:00
abstract：:Signal transduction pathways often modulate both positively and negatively acting components to optimize the efficiency of a signal. Recent results have shown that plants make extensive use of regulated proteolysis to modulate signal transduction pathways. An emerging theme from hormone (e.g. auxin and gibberellin) an...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2005.11.005
更新日期：2006-01-01 00:00:00
abstract：:The highly photosynthetic-efficient C4 grasses, such as switchgrass (Panicum virgatum), Miscanthus (Miscanthusxgiganteus), sorghum (Sorghum bicolor) and maize (Zea mays), are expected to provide abundant and sustainable resources of lignocellulosic biomass for the production of biofuels. A deeper understanding of the ...
journal_title：Trends in plant science
pub_type： 杂志文章
doi：10.1016/j.tplants.2008.06.002
更新日期：2008-08-01 00:00:00
abstract：:Plastid endosymbiosis was accompanied by the appearance of a novel type of semi-cristalline storage polysaccharide (starch). Interestingly, starch is found in the cytoplasm of Rhodophyceae and Glaucophyta but is localized to the chloroplast stroma of Chloroplastida. The pathway is presumed to have been cytosolic in th...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2008.08.009
更新日期：2008-11-01 00:00:00
abstract：:The plant fungal pathogen Fusarium oxysporum (Fox) is the causal agent of root rot or wilt diseases in several plant species, including crops such as tomato (Solanum lycopersicum), banana (Musa sapientum) and asparagus (Asparagus officinalis). Colonization of plants by Fox leads to the necrosis of the infected tissues...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2007.12.004
更新日期：2008-03-01 00:00:00
abstract：:The evolution of land plants approximately 470 million years ago created a new adaptive zone for natural enemies (attackers) of plants. In response to attack, plants evolved highly effective, inducible defense systems. Two plant hormones modulating inducible defenses are salicylic acid (SA) and jasmonic acid (JA). Cur...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2012.02.010
更新日期：2012-05-01 00:00:00
abstract：:Recent methodological advances have uncovered tremendous microbial diversity cohabiting in the same host plant, and many of these microbes cause disease. In this review we highlight how the presence of other pathogen species, or other pathogen genotypes, within a plant can affect key components of host-pathogen intera...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2015.10.014
更新日期：2016-01-01 00:00:00
abstract：:Recently established links between the tomato cyclophilin A-type protein DIAGEOTROPICA and the regulation of polar auxin transport provide first mechanistic insights into the function of this enigmatic locus. ...
journal_title：Trends in plant science
pub_type： 评论,杂志文章
doi：10.1016/j.tplants.2015.04.009
更新日期：2015-06-01 00:00:00
abstract：:A limiting factor for photosynthetic organisms is their light-harvesting efficiency, that is the efficiency of their conversion of light energy to chemical energy. Small modifications or variations of chlorophylls allow photosynthetic organisms to harvest sunlight at different wavelengths. Oxygenic photosynthetic orga...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2011.03.011
更新日期：2011-08-01 00:00:00
abstract：:Plants have evolved a large number of cell surface-resident receptor-like kinases (RLKs) and receptor-like proteins (RLPs), many of which are implicated in sensing extrinsic and intrinsic signals, and govern diverse cellular responses. The signaling pathways mediated by RLKs and RLPs converge at a small group of RLKs,...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2016.08.014
更新日期：2016-12-01 00:00:00
abstract：:The plant-specific LBD (Lateral Organ Boundaries Domain) gene family is essential in the regulation of plant lateral organ development and is involved in the regulation of anthocyanin and nitrogen metabolism. LBD proteins contain a characteristic LOB domain composed of a C-motif required for DNA-binding, a conserved g...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2010.09.009
更新日期：2011-01-01 00:00:00
abstract：:Serine (Ser) has a fundamental role in metabolism and signaling in living organisms. In plants, the existence of different pathways of Ser biosynthesis has complicated our understanding of this amino acid homeostasis. The photorespiratory glycolate pathway has been considered to be of major importance, whereas the non...
journal_title：Trends in plant science
pub_type： 杂志文章
doi：10.1016/j.tplants.2014.06.003
更新日期：2014-09-01 00:00:00
abstract：:To understand how DNA sequence is translated to phenotype we must understand the epigenetic features that regulate gene expression. Recent research illuminates the complex interactions between DNA methylation, small RNAs, silencing of transposable elements, and genomic imprinting in the Arabidopsis (Arabidopsis thalia...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2010.01.002
更新日期：2010-04-01 00:00:00
abstract：:To exploit plants as living substrates, biotrophic fungi have evolved remarkable variations of their tubular cells, the hyphae. They form infection structures such as appressoria, penetration hyphae and infection hyphae to invade the plant with minimal damage to host cells. To establish compatibility with the host, co...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/s1360-1385(02)02297-5
更新日期：2002-08-01 00:00:00
abstract：:Faced with an accelerating rate of environmental change and the associated need for a more sustainable, low-input agriculture, the urgent new challenge for crop science is to find ways to introduce greater diversity to cropping systems. However, there is a dearth of generic formalism in programs seeking to diversify c...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2015.07.007
更新日期：2015-10-01 00:00:00
abstract：:Acquired tolerance to temperature stresses is a major protective mechanism. Recent advances have revealed key components of stress signal transduction pathways that trigger enhanced tolerance, and several determinants of acquired tolerance have been identified. Although high and low temperature stresses impose differe...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/S1360-1385(03)00047-5
更新日期：2003-04-01 00:00:00
abstract：:The grey mould Botrytis cinerea causes disease in more than 1000 plant species, including important crops. The interaction between Botrytis and its (potential) hosts is determined by quantitative susceptibility and virulence traits in both interacting partners, resulting in a greyscale of disease outcomes. Fungal infe...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2018.03.016
更新日期：2018-07-01 00:00:00
abstract：:The amount of sequence data available to reconstruct the evolutionary history of genes and species has increased 20-fold in the past decade. Consequently the size of phylogenetic analyses has grown as well, and phylogenetic methods, algorithms and their implementations have struggled to keep pace. Computational and ot...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/S1360-1385(03)00165-1
更新日期：2003-08-01 00:00:00
abstract：:Plant-derived pharmaceuticals are poised to become the next major commercial development in biotechnology. The advantages they offer in terms of production scale and economy, product safety, ease of storage and distribution cannot be matched by any current commercial system; they also provide the most promising opport...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2005.10.009
更新日期：2005-12-01 00:00:00
abstract：:The members of the pathogenesis-related protein 1 (PR-1) family are among the most abundantly produced proteins in plants on pathogen attack, and PR-1 gene expression has long been used as a marker for salicylic acid-mediated disease resistance. However, despite considerable interest over several decades, their requir...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2017.06.013
更新日期：2017-10-01 00:00:00
abstract：:Following the sequencing of whole genomes of model plants, high-throughput decoding of gene function is a major challenge in modern plant biology. In view of remarkable technical advances in transcriptomics and metabolomics, integrated analysis of these 'omics' by data-mining informatics is an excellent tool for predi...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2007.10.006
更新日期：2008-01-01 00:00:00
abstract：:Plants form diverse symbioses with nitrogen-fixing bacteria to gain access to ammonium, a product of the prokaryote-exclusive enzyme nitrogenase. Improving the symbiotic effectiveness of crop plants like maize, wheat or rice is a highly topical challenge and could help reduce the need for energy-intense nitrogen ferti...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2008.11.009
更新日期：2009-02-01 00:00:00
abstract：:Unless there are mechanisms to selectively retain membrane proteins in the endoplasmic reticulum (ER) or in the Golgi apparatus, they automatically proceed downstream to the plasma or vacuole membranes. Two types of coat protein complex I (COPI)-interacting motifs in the cytosolic tails of membrane proteins seem to fa...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2014.04.004
更新日期：2014-08-01 00:00:00
abstract：:In spite of the large yield losses that weeds inflict on crops, we know little about the genomics of economically important weed species. Comparative genomics between plant model species and weeds, map-based approaches, genomic sequencing and functional genomics can play vital roles in understanding and dissecting wee...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2004.06.003
更新日期：2004-08-01 00:00:00
abstract：:Higher plants are constructed of three organs--the stem, the root and the leaf. The stem and the root have two axes, apical-basal and central-peripheral, which cross orthogonally. Leaves develop from the shoot apical meristem as lateral organs that have three different axes, apical-basal, adaxial-abaxial and right-lef...
journal_title：Trends in plant science
pub_type： 新闻
doi：10.1016/s1360-1385(01)02155-0
更新日期：2001-12-01 00:00:00
abstract：:The infection and replication of viruses in the host induce diverse mechanisms for combating viral infection. One of the best-studied antiviral defence mechanisms is based on RNA silencing. Consistently, several viral suppressors of RNA silencing (VSRs) have been identified from almost all plant virus genera, which ar...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2011.02.010
更新日期：2011-05-01 00:00:00
abstract：:Until recently, few data were available on photosynthesis and its underlying mechanistically limiting factors in plants, other than crops and model species. Currently, a new large pool of data from extant representatives of basal terrestrial plant groups is emerging, allowing exploration of how photosynthetic capacity...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2019.07.002
更新日期：2019-10-01 00:00:00
abstract：:A range of bio- and nanotechnologies have been developed that could be adapted towards monitoring the presence and expression of transgenes, in real time and in the field, in plants of agronomic and ecological importance. Transgene escape from crop hosts to wild relatives or landraces is one example in which monitorin...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2005.06.003
更新日期：2005-08-01 00:00:00
abstract：:The intricate, heavily folded inner membrane of mitochondria houses the respiratory chain complexes. These complexes, together with the ATP synthase complex, are responsible for energy production, which is stored as ATP. The structure of the individual membrane-bound protein components has been well characterized. In ...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2006.03.007
更新日期：2006-05-01 00:00:00
abstract：:Natural genetic variation within plant species is at the core of plant science ranging from agriculture to evolution. Whereas much progress has been made in mapping quantitative trait loci (QTLs) controlling this natural variation, the elucidation of the underlying molecular mechanisms has remained a bottleneck. Recen...
journal_title：Trends in plant science
pub_type： 杂志文章,评审
doi：10.1016/j.tplants.2007.11.008
更新日期：2008-02-01 00:00:00
