自引率: 3.1%
被引量: 9595
通过率: 暂无数据
审稿周期: 2.63
版面费用: 暂无数据
国人发稿量: 26
投稿须知/期刊简介:
The goal of Genomics is the promotion of all facets of human/mouse genetic analysis. The scope of the journal is broad, and studies of other species that provide important insights into gene function in mouse/human will be considered. The editors welcome
期刊描述简介:
Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope. Topics within the scope of Genomics include, but are not limited to: • Genomics including genome projects, genome sequencing, and genomic technologies and novel strategies. • Functional genomics including transcriptional profiling, mRNA analysis, microRNA analysis, and analysis of noncoding and other RNAs using established and newly-emerging technologies (such as digital gene expression). • Evolutionary and comparative genomics, including phylogenomics • Genomic technology and methodology development, with a focus on new and exciting applications with potential for significant impact in the field and emerging technologies • Computational biology, bioinformatics and biostatistics, including integrative methods, network biology, and the development of novel tools and techniques • Modern genetics on a genomic scale, including complex gene studies, population genomics, association studies, structural variation, and gene-environment interactions • Epigenomics, including DNA methylation, histone modification, chromatin structure, imprinting, and chromatin remodeling • Genomic regulatory analysis, including DNA elements, locus control regions, insulators, enhancers, silencers, and mechanisms of gene regulation • Genomic approaches to understanding the mechanism of disease pathogenesis and its relationship to genetic factors, including meta-genomic and the mode and tempo of gene and genome sequence evolution. • Medical Genomics, Personal Genomics, and other applications to human health • Application of Genomic techniques in model organisms that may be of interest to a wide audience. • RNA-seq experiments without biological replicates will not be accepted for differential expression–based articles. Genomics primarily publishes original research articles but also welcomes proposals for full-length and mini reviews. All submissions to Genomics are subject to rigorous peer review and our goal is to accept only the top 25-30% of submitted manuscripts. Please contact the Editorial Office with review proposals or any inquiries regarding the scope of the journal or the suitability of a manuscript for publication.
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Signatures of selection in Nelore cattle revealed by whole-genome sequencing data.
Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value<0.05), and 718 segments were target as signatures of selection. A total of 1713 highly differentiated genomic regions were identified based on the segmentFst approach. The signatures of selection were spread across the genome. Annotation of overlapping selection signature regions between the two methods revealed 118 genes in common. A variant located within the 3' region of the BOLA-DRB3 gene was found as a promising candidate polymorphism. Within genomic regions that deserves attention, we found genes previously associated with adaptation to tropical environments (HELB), growth and navel size (HMGA2), fat deposition and domestication (IRAK3), and feed efficiency and postmortem carcass traits (GABRG3). The genes BOLA-DQA2, BOLA-DQB, BOLA-DQA5, BOLA-DQA1, BOLA-DRB3, ENSBTAG00000038397 on chromosome 23 are part of the Bovine Major Histocompatibility Complex (MHC) Class II gene family, representing good candidates for immune response and adaptation to tropical conditions. The BoLA family genes and the interaction of ROBO1 with SLIT genes appeared in the enrichment results. Genomic regions located in intronic regions were also identified and might play a regulatory role in traits under selection in PO and CEIP subpopulations. The regions here identified contribute to our knowledge regarding genes and variants that have an important role in complex traits selected in this breed.
被引量：5 发表：1970
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Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses.
Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high. Various polishing algorithms using Illumina short reads to correct the errors in Oxford Nanopore long-read assemblies have been developed. The impact of polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads on improving genomic analyses was evaluated using both simulated and real reads. Ten species (10 strains) were selected for simulated reads, while real reads were tested on 11 species (11 strains). Oxford Nanopore long reads were assembled with Unicycler to produce a draft assembly, followed by three rounds of polishing with Illumina short reads using two polishing tools, Pilon and NextPolish. One round of NextPolish polishing generated genome completeness and accuracy parameters similar to the reference genomes, whereas two or three rounds of Pilon polishing were needed, though contiguity remained unchanged after polishing. The polished assemblies of Escherichia coli O157:H7, Salmonella Typhimurium, and Cronobacter sakazakii with simulated reads did not provide accurate plasmid identifications. One round of NextPolish polishing was needed for accurately identifying plasmids in Staphylococcus aureus and E. coli O26:H11 with real reads, whereas one and two rounds of Pilon polishing were necessary for these two strains, respectively. Polishing failed to provide an accurate antimicrobial resistance (AMR) genotype for S. aureus with real reads. One round of polishing recovered an accurate AMR genotype for Klebsiella pneumoniae with real reads. The reference genome and draft assembly of Citrobacter braakii with real reads differed, which carried blaCMY-83 and fosA6, respectively, while both genes were present after one round of polishing. However, polishing did not improve the assembly of E. coli O26:H11 with real reads to achieve numbers of virulence genes similar to the reference genome. The draft and polished assemblies showed a phylogenetic tree topology comparable with the reference genomes. For multilocus sequence typing and pan-genome analyses, one round of NextPolish polishing was sufficient to obtain accurate results, while two or three rounds of Pilon polishing were needed. Overall, NextPolish outperformed Pilon for polishing the Oxford Nanopore long-read assemblies of bacterial pathogens, though both polishing strategies improved genomic analyses compared to the draft assemblies.
被引量：22 发表：1970
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Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle.
Milk production and composition are the most economically important traits affecting profitability in dairy cattle. In this study, we aimed at detecting signatures of positive selection in Kenana, known as one of the high milk production African indigenous zebu cattle, using next-generation sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (F), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (Pi). Further analysis showed that several candidate genes such as CSN3, IGFBP-2, RORA, ABCG2, B4GALT1 and GHR are positively selected for milk production traits in Kenana cattle. The candidate genes and enriched pathways identified in this study may provide a basis for future genome-wide association studies and investigations into genomic targets of selection in dairy cattle.
被引量：9 发表：1970
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Gastrocnemius transcriptome analysis reveals domestication induced gene expression changes between wild and domestic chickens.
Artificial selection of chicken for human-preferred traits has manifested great phenotypic differences between wild and domestic chickens. Study on the formation of these phenotypic variations will contribute to comprehensive understanding of the molecular mechanism of animal domestication. We used three kinds of chicken breeds for transcriptome analysis, including the red jungle fowl which was the wild ancestor of chickens, and two other domestic breeds, the chahua chicken and the avian broiler. More than 12,000 genes' expression levels were compared between different chicken breeds, and hundreds of genes displayed differential expression levels compared with wild chicken. Gene ontology analysis showed that differentially expressed genes in domestic chickens tended to be enriched in extracellular matrix, DNA binding and immune system development, etc. Some genes with important biological functions were differentially expressed in the domestic chickens, including titin, myostatin ubiquitin related genes, and transforming growth factor-beta receptor III, indicating possible selection pressures on these genes.
被引量：11 发表：1970
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Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing.
Several miRNA family and their targets in cotton had been identified by computational methods based on the conserved characterization of miRNAs. So far, there are no experiments to validate the existence of miRNAs in cotton. In this study, to analyze the miRNAs in cotton, a small RNA library of sequences from 18 to 26 nt of Gossypium hirsutum seedling has been built by high-throughput sequencing. In this library, 34 conserved miRNA families were identified by homology search and the miRNA sequences of them were also found in the library. Furthermore, potential targets of these conserved miRNA families were predicted in cotton TC library. However, based on the mature miRNAs and their miR sequences, only 8 conserved miRNA encoding loci (miR156, miR157a, miR157b, miR162, miR164, miR393, miR399, miR827) were identified from cotton EST sequences. Multiple encoding loci of some miRNAs were identified by comparing the cloned miRNA and miR sequences.
被引量：- 发表：1970
