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Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri. The two genomes were assembled to a chromosome level using PacBio long-read technology, HiC, and Bionano optical mapping. This report corrects some minor assembly errors found in the Sanger assembly of G. raimondii. We also compare the genome sequences of these two species for gene composition, repetitive element composition, and collinearity. Most of the identified structural rearrangements between these two species are due to intra-chromosomal inversions. More inversions were found in the G. turneri genome sequence than the G. raimondii genome sequence. These findings and updates to the D-genome sequence will improve accuracy and translation of genomics to cotton breeding and genetics.

Microorganisms, genetically modified or not, may be used in the food chain as such or as production organisms of substances of interest. The placement of such microorganisms or derived substances/products in the European market may be subject to a pre‐market authorisation process. The authorisation process defines the need to perform a risk assessment to establish the safety and/or the efficacy of the microorganisms when used in the food chain as such or as production strains of substances of interest. In order to perform a risk assessment, the microorganism/s subject to the application for authorisation need/s to be characterised. In this regard, data obtained from whole genome sequence analysis can provide information on the unequivocal taxonomic identification of the strains and on the characterisation of their potential functional traits of concern which may include virulence factors, resistance to antimicrobials of clinical relevance for humans and animals, production of known toxic metabolites. In fact, in some areas of the regulated products, the use of whole genome sequence‐based data has been established as a requirement for the risk assessment. This document provides recommendations to applicants on how to describe the process and results which should be provided to the risk assessor in the context of an application for market authorisation of a regulated product. Indications are given on how to perform WGS and the quality criteria/thresholds that should be reached as well as the data and relevant information that need to be sent along whenever such kind of data is required.

Through imputation of genotypes, genome‐wide association study (GWAS) and genomic prediction (GP) using whole‐genome sequencing (WGS) data are cost‐efficient and feasible in aquaculture breeding schemes. The objective was to dissect the genetic architecture of growth traits under chronic heat stress in rainbow trout (Oncorhynchus mykiss) and to assess the accuracy of GP based on imputed WGS and different preselected single nucleotide polymorphism (SNP) arrays. A total of 192 and 764 fish challenged to a heat stress experiment for 62 days were genotyped using a customized 1 K and 26 K SNP panels, respectively, and then, genotype imputation was performed from a low‐density chip to WGS using 102 parents (36 males and 66 females) as the reference population. Imputed WGS data were used to perform GWAS and test GP accuracy under different preselected SNP scenarios. Heritability was estimated for body weight (BW), body length (BL) and average daily gain (ADG). Estimates using imputed WGS data ranged from 0.33 ± 0.05 to 0.55 ± 0.05 for growth traits under chronic heat stress. GWAS revealed that the top five cumulatively SNPs explained a maximum of 0.94%, 0.86% and 0.51% of genetic variance for BW, BL and ADG, respectively. Some important functional candidate genes associated with growth‐related traits were found among the most important SNPs, including signal transducer and activator of transcription 5B and 3 (STAT5B and STAT3, respectively) and cytokine‐inducible SH2‐containing protein (CISH). WGS data resulted in a slight increase in prediction accuracy compared with pedigree‐based method, whereas preselected SNPs based on the top GWAS hits improved prediction accuracies, with values ranging from 1.2 to 13.3%. Our results support the evidence of the polygenic nature of growth traits when measured under heat stress. The accuracies of GP can be improved using preselected variants from GWAS, and the use of WGS marginally increases prediction accuracy.

Background Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences. Result Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage. Conclusion Our study provides objective feature sets in constructing evolution relationships at the genomic level.

Microorganisms, genetically modified or not, may be used in the food chain either as active agents, biomasses or as production organisms of substances of interest. The placement of such microorganisms or their derived substances/products in the European market may be subject to a premarket authorisation process. The authorisation process requires a risk assessment in order to establish the safety and/or the efficacy of the microorganism(s) when used in the food chain as such, as biomasses or as production strains. This includes a full molecular characterisation of the microorganism(s) under assessment. For certain regulated products, the use of whole genome sequence (WGS) data of the microorganism is established as a requirement for the risk assessment. In this regard, data obtained from WGS analysis can provide information on the unambiguous taxonomic identification of the strains, on the presence of genes of concern (e.g. those encoding virulence factors, resistance to antimicrobials of clinical relevance for humans and animals, production of harmful metabolites or of clinically relevant antimicrobials) and on the characterisation of genetic modification(s) (where relevant). This document provides recommendations to applicants on how to describe and report the results of WGS analyses in the context of an application for market authorisation of a regulated product. Indications are given on how to perform genome sequencing and the quality criteria/thresholds that should be reached, as well as the data and relevant information that need to be reported, if required. This updated document replaces the EFSA 2021 Statement and reflects the current knowledge in technologies and methodologies to be used to generate and analyse WGS data for the risk assessment of microorganisms.

The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea‐Bissau (GB), the subspecies is increasingly threatened, but there is a lack of understanding regarding the degree of genetic threat faced by populations. This hinders the development of targeted conservation strategies and the prioritization of efforts by national agencies. In this study, we use microsatellite data from four parks located in southern GB and five whole‐genome sequences to estimate the effective population size (Ne) and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss the strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10,000–15,000 years ago. After that, a change in connectivity, a real decrease in size, or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: ~10,000 decreasing to 1,000–6,000 breeding individuals), possibly indicating a fragmentation into coastal and inland subpopulations. In the most recent past, contemporary Ne is close to 500 (GONE: 395–583, NeEstimator: 107–549), suggesting a high risk of extinction. The populations located at the coastal parks may have been small or isolated for several generations and are at higher risk, whereas the ones located inland exhibit higher long‐term Ne and can be considered a stronghold for chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we tried to overcome the limitations of obtaining high‐quality DNA samples from wild threatened populations and estimated Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro‐pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.

Rice blast, caused by Magnaporthe oryzae , is one of the most devastating diseases affecting rice crops. We investigated effectiveness of Streptomyces spp. against M. oryzae . The results revealed that among the Streptomyces spp., Streptomyces caeruleatus strain S14 demonstrated superior effectiveness in inhibiting the mycelial growth of M. oryzae (74.7%). The strain was identified by sequencing 16S rRNA region. Further, the complete genome sequence of this highly effective strain was acquired using the Illumina NovaSeq 6000 (PE 150), revealing a total genome length of 9,750,804 base pairs (9.7 Mb). The genome comprises 9,191 protein-coding sequences (CDS), 68 transfer RNA (tRNA) genes, 6 ribosomal RNA (rRNA) genes, with an average G+C content of 71.03%. The Streptomyces caeruleatus S14 genome, annotated with RASTtk and genetic code 11, falls under the superkingdom Bacteria. According to annotation statistics from PATRIC, it is a high-quality genome with 97.9% coarse consistency, 93.7% fine consistency, and completeness of 99.9%. The genome included genes related to metabolism, protein processing, defense, virulence, energy, stress response, membrane transport, regulation, cell signaling, cell envelope, DNA processing, cellular activities, RNA processing, and miscellaneous. The complete genome sequence of S. caeruleatus suggests that it offers valuable insights into its antimicrobial activity and provide key genetic traits responsible for pathogen suppression. Incidentally this is the first whole genome sequencing report of S. caeruleatus isolated from rice rhizosphere soil in India.

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome—composed of approximately one billion base pairs of sequence and an estimated 20,000–23,000 genes—provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.