Huazhong Agricultural University

We describe "universal" DNA primers for polymerase chain reaction (PCR) amplification of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from 11 invertebrate phyla: Echinodermata, Mollusca, Annelida, Pogonophora, Arthropoda, Nemertinea, Echiura, Sipuncula, Platyhelminthes, Tardigrada, and Coelenterata, as well as the putative phylum Vestimentifera. Preliminary comparisons revealed that these COI primers generate informative sequences for phylogenetic analyses at the species and higher taxonomic levels.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus , which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia , Amylolactobacillus , Bombilactobacillus , Companilactobacillus , Lapidilactobacillus , Agrilactobacillus , Schleiferilactobacillus , Loigolactobacilus , Lacticaseibacillus , Latilactobacillus , Dellaglioa , Liquorilactobacillus , Ligilactobacillus , Lactiplantibacillus , Furfurilactobacillus , Paucilactobacillus , Limosilactobacillus , Fructilactobacillus , Acetilactobacillus , Apilactobacillus , Levilactobacillus , Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae . The generic term ‘lactobacilli’ will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii , Lactobacillus iners , Lactobacillus crispatus , Lactobacillus jensensii , Lactobacillus johnsonii and <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.5326" xlink:type

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Abiotic stresses are one of the major constraints to crop production and food security worldwide. The situation has aggravated due to the drastic and rapid changes in global climate. Heat and drought are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical, and ecological interventions related to these stresses for better management. A wide range of plant responses to these stresses could be generalized into morphological, physiological, and biochemical responses. Interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. Crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions, and biochemical changes. Both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. A better understanding of plant responses to these stresses has pragmatic implication for remedies and management. A comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. A side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. A holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future.

The impact of projected global warming on crop yields has been evaluated by indirect methods using simulation models. Direct studies on the effects of observed climate change on crop growth and yield could provide more accurate information for assessing the impact of climate change on crop production. We analyzed weather data at the International Rice Research Institute Farm from 1979 to 2003 to examine temperature trends and the relationship between rice yield and temperature by using data from irrigated field experiments conducted at the International Rice Research Institute Farm from 1992 to 2003. Here we report that annual mean maximum and minimum temperatures have increased by 0.35 degrees C and 1.13 degrees C, respectively, for the period 1979-2003 and a close linkage between rice grain yield and mean minimum temperature during the dry cropping season (January to April). Grain yield declined by 10% for each 1 degrees C increase in growing-season minimum temperature in the dry season, whereas the effect of maximum temperature on crop yield was insignificant. This report provides a direct evidence of decreased rice yields from increased nighttime temperature associated with global warming.

Environmental problems have always received immense attention from scientists. Toxicants pollution is a critical environmental concern that has posed serious threats to human health and agricultural production. Heavy metals and pesticides are top of the list of environmental toxicants endangering nature. This review focuses on the toxic effect of heavy metals (cadmium (Cd), lead (Pb), copper (Cu), and zinc (Zn)) and pesticides (insecticides, herbicides, and fungicides) adversely influencing the agricultural ecosystem (plant and soil) and human health. Furthermore, heavy metals accumulation and pesticide residues in soils and plants have been discussed in detail. In addition, the characteristics of contaminated soil and plant physiological parameters have been reviewed. Moreover, human diseases caused by exposure to heavy metals and pesticides were also reported. The bioaccumulation, mechanism of action, and transmission pathways of both heavy metals and pesticides are emphasized. In addition, the bioavailability in soil and plant uptake of these contaminants has also been considered. Meanwhile, the synergistic and antagonistic interactions between heavy metals and pesticides and their combined toxic effects have been discussed. Previous relevant studies are included to cover all aspects of this review. The information in this review provides deep insights into the understanding of environmental toxicants and their hazardous effects.

Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. The genome of the potato (Solanum tuberosum L.), a staple crop vital to food security, has been sequenced. The Potato Genome Sequencing Consortium sequenced a homozygous doubled-monoploid potato clone as well as a heterozygous diploid clone. Genome analysis reveals traces of at least two genome duplication events and genes specific to Asterids, a large clade of flowering plants of which the potato is the first to be sequenced. Gene presence/absence variants and other potentially deleterious mutations are frequent and may be the cause of inbreeding depression. The genome sequence will facilitate genetic improvements in the potato with a view to improving yield and to increasing disease and stress resistance of this crop, which is a now a significant component of worldwide food production and is becoming increasingly important in the developing world.

The review summarizes the recent progress in the synthesis, fundamental properties, morphology, photocatalytic applications and challenges of CdS-based photocatalysts.

False positives in a Genome-Wide Association Study (GWAS) can be effectively controlled by a fixed effect and random effect Mixed Linear Model (MLM) that incorporates population structure and kinship among individuals to adjust association tests on markers; however, the adjustment also compromises true positives. The modified MLM method, Multiple Loci Linear Mixed Model (MLMM), incorporates multiple markers simultaneously as covariates in a stepwise MLM to partially remove the confounding between testing markers and kinship. To completely eliminate the confounding, we divided MLMM into two parts: Fixed Effect Model (FEM) and a Random Effect Model (REM) and use them iteratively. FEM contains testing markers, one at a time, and multiple associated markers as covariates to control false positives. To avoid model over-fitting problem in FEM, the associated markers are estimated in REM by using them to define kinship. The P values of testing markers and the associated markers are unified at each iteration. We named the new method as Fixed and random model Circulating Probability Unification (FarmCPU). Both real and simulated data analyses demonstrated that FarmCPU improves statistical power compared to current methods. Additional benefits include an efficient computing time that is linear to both number of individuals and number of markers. Now, a dataset with half million individuals and half million markers can be analyzed within three days.

Drought and salinity are major abiotic stresses to crop production. Here, we show that overexpression of stress responsive gene SNAC1 (STRESS-RESPONSIVE NAC 1) significantly enhances drought resistance in transgenic rice (22-34% higher seed setting than control) in the field under severe drought stress conditions at the reproductive stage while showing no phenotypic changes or yield penalty. The transgenic rice also shows significantly improved drought resistance and salt tolerance at the vegetative stage. Compared with WT, the transgenic rice are more sensitive to abscisic acid and lose water more slowly by closing more stomatal pores, yet display no significant difference in the rate of photosynthesis. SNAC1 is induced predominantly in guard cells by drought and encodes a NAM, ATAF, and CUC (NAC) transcription factor with transactivation activity. DNA chip analysis revealed that a large number of stress-related genes were up-regulated in the SNAC1-overexpressing rice plants. Our data suggest that SNAC1 holds promising utility in improving drought and salinity tolerance in rice.

Plants are subjected to various environmental stresses throughout their life cycle. Reactive oxygen species (ROS) play important roles in maintaining normal plant growth, and improving their tolerance to stress. This review describes the production and removal of ROS in plants, summarizes recent progress in understanding the role of ROS during plant vegetative apical meristem development, organogenesis, and abiotic stress responses, and some novel findings in recent years are discussed. More importantly, interplay between ROS and epigenetic modifications in regulating gene expression is specifically discussed. To summarize, plants integrate ROS with genetic, epigenetic, hormones and external signals to promote development and environmental adaptation.

Abstract Exploring photocatalysts to promote CO 2 photoreduction into solar fuels is of great significance. We develop TiO 2 /perovskite (CsPbBr 3 ) S-scheme heterojunctions synthesized by a facile electrostatic-driven self-assembling approach. Density functional theory calculation combined with experimental studies proves the electron transfer from CsPbBr 3 quantum dots (QDs) to TiO 2 , resulting in the construction of internal electric field (IEF) directing from CsPbBr 3 to TiO 2 upon hybridization. The IEF drives the photoexcited electrons in TiO 2 to CsPbBr 3 upon light irradiation as revealed by in-situ X-ray photoelectron spectroscopy analysis, suggesting the formation of an S-scheme heterojunction in the TiO 2 /CsPbBr 3 nanohybrids which greatly promotes the separation of electron-hole pairs to foster efficient CO 2 photoreduction. The hybrid nanofibers unveil a higher CO 2 -reduction rate (9.02 μmol g –1 h –1 ) comparing with pristine TiO 2 nanofibers (4.68 μmol g –1 h –1 ). Isotope ( 13 CO 2 ) tracer results confirm that the reduction products originate from CO 2 source.

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. This study presents the assembly and analysis of the genome sequence of a female domestic Duroc pig and a comparison with the genomes of wild and domestic pigs from Europe and Asia; the results shed light on the evolutionary relationship between European and Asian wild boars. The domestic pig (Sus scrofa) is an important livestock species, its genome shaped by thousands of years of domestication and, latterly, sophisticated breeding practices. A high-quality draft genome sequence for a female domestic Duroc pig is published in this issue of Nature, under the auspices of the Swine Genome Sequencing Consortium. Comparisons of the genomes of wild and domestic pigs shed light on the evolutionary relationship between European and Asian wild boars, and reveal the rapid evolution of genes involved in the immune response and in olfaction. The authors identify many possible disease-causing gene variants, increasing the potential of the pig as a biomedical model, and present a detailed analysis of endogenous porcine retroviruses, knowledge of which is important for the possible use of pigs in xenotransplantation.

Along with the development of high-throughput sequencing technologies, both sample size and SNP number are increasing rapidly in genome-wide association studies (GWAS), and the associated computation is more challenging than ever. Here, we present a memory-efficient, visualization-enhanced, and parallel-accelerated R package called "rMVP" to address the need for improved GWAS computation. rMVP can 1) effectively process large GWAS data, 2) rapidly evaluate population structure, 3) efficiently estimate variance components by Efficient Mixed-Model Association eXpedited (EMMAX), Factored Spectrally Transformed Linear Mixed Models (FaST-LMM), and Haseman-Elston (HE) regression algorithms, 4) implement parallel-accelerated association tests of markers using general linear model (GLM), mixed linear model (MLM), and fixed and random model circulating probability unification (FarmCPU) methods, 5) compute fast with a globally efficient design in the GWAS processes, and 6) generate various visualizations of GWAS-related information. Accelerated by block matrix multiplication strategy and multiple threads, the association test methods embedded in rMVP are significantly faster than PLINK, GEMMA, and FarmCPU_pkg. rMVP is freely available at https://github.com/xiaolei-lab/rMVP.

Dissolution of cellulose with ionic liquids allows the comprehensive utilization of cellulose by combining two major green chemistry principles: using environmentally preferable solvents and bio-renewable feed-stocks. In this paper, the dissolution of cellulose with ionic liquids and its application were reviewed. Cellulose can be dissolved, without derivation, in some hydrophilic ionic liquids, such as 1-butyl-3-methylimidazolium chloride (BMIMCl) and 1-allyl-3-methylimidazolium chloride (AMIMCl). Microwave heating significantly accelerates the dissolution process. Cellulose can be easily regenerated from its ionic liquid solutions by addition of water, ethanol or acetone. After its regeneration, the ionic liquids can be recovered and reused. Fractionation of lignocellulosic materials and preparation of cellulose derivatives and composites are two of its typical applications. Although some basic studies, such as economical syntheses of ionic liquids and studies of ionic liquid toxicology, are still much needed, commercialization of these processes has made great progress in recent years.

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. Brassica oleracea is plant species comprising economically important vegetable crops. Here, the authors report the draft genome sequence of B. oleracea and, through a comparative analysis with the closely related B. rapa, reveal insights into Brassicaevolution and divergence of interspecific genomes and intraspecific subgenomes.