Bov-A2 is a retroposon that is widely distributed among the genomes of ruminants (e.g., cow, deer, giraffe, pronghorn, musk deer, and chevrotain). This retroposon is composed of two monomers, called Bov-A units, which are joined by a linker sequence. The structure and origin of Bov-A2 has been well characterized but a genome-level exploration of this retroposon has not been implemented. In this study we performed an extensive search for Bov-A2 using all available genome sequence data on Bos taurus. We found unique Bov-A2-derived sequences that were longer than Bov-A2 due to amplification of three to six Bov-A units arranged in tandem. Detailed analysis of these elongated Bov-A2-derived sequences revealed that they originated through unequal crossing-over of Bov-A2. We found a large number of these elongated Bov-A2-derived sequences in cattle genomes, indicating that unequal crossing-over of Bov-A2 occurred very frequently. We found that this type of elongation is not observed in wild bovine and is therefore specific to the domesticated cattle genome. Furthermore, at specific loci, the number of Bov-A units was also polymorphic between alleles, implying that the elongation of Bov-A units might have occurred very recently. For these reasons, we speculate that genomic instability in bovine genomes can lead to extensive unequal crossing-over of Bov-A2 and levels of polymorphism might be generated in part by repeated outbreeding.
Fumonisins are well known as mycotoxins produced by various Fusarium species. Recently Aspergillus niger has been reported to be a fumonisin B 2 (FB 2 ) producer. Aspergillus niger is a member of Aspergillus section Nigri. Members of this section are common food contaminants and are also distributed widely in the environment. This study aimed to determine 1) optimum culture conditions of A. niger for fumonisin production including growth medium, temperature and incubation period and 2) fumonisin production among isolates of Aspergillus section Nigri and closely related species isolated from Japanese food and environmental samples. Growth on Czapek yeast extract broth +5% NaCl (CYBS) at 28°C for 7 days resulted in the highest levels of FB 2 production as determined by quantitative LC-MS/MS of culture extracts. Sixty-two isolates were collected from various foods in domestic markets as well as from soil and air. The isolates principally separated into two groups; A. niger and A. luchuensis/A. piperis/A. tubingensis, following molecular phylogenetic analysis. ELISA using the tip culture method was shown to be suitable for screening of the fumonisin-producing strains. Phylogenic analysis of Aspergillus section Nigri isolates from food and environmental samples indicated that fumonisin producing strains could be grouped into the A. niger clade. Nineteen of 35 (54%) isolates classified as A. niger were FB 2 producers. The current study suggests that FB 2 -producing A. niger are distributed throughout several regions of Japan.
49The volume of biological database records is growing rapidly, populated by complex records 50 drawn from heterogeneous sources. A specific challenge is duplication, that is, the presence of 51 redundancy (records with high similarity) or inconsistency (dissimilar records that correspond to 52 the same entity). The characteristics (which records are duplicates), impact (why duplicates are 53 significant), and solutions (how to address duplication), are not well understood. Studies on the 54 topic are neither recent nor comprehensive. In addition, other data quality issues, such as 55 inconsistencies and inaccuracies, are also of concern in the context of biological databases. A 56 primary focus of this paper is to present and consolidate the opinions of over 20 experts and 57 practitioners on the topic of duplication in biological sequence databases. The results reveal that 58 survey participants believe that duplicate records are diverse; that the negative impacts of 59 duplicates are severe, while positive impacts depend on correct identification of duplicates; and 60 that duplicate detection methods need to be more precise, scalable, and robust. A secondary 61 focus is to consider other quality issues. We observe that biocuration is the key mechanism used 62 3 to ensure the quality of this data, and explore the issues through a case study of curation in 63 UniProtKB/Swiss-Prot as well as an interview with an experienced biocurator. While biocuration 64 is a vital solution for handling of data quality issues, a broader community effort is needed to 65 provide adequate support for thorough biocuration in the face of widespread quality concerns. 66 67 68 69 The major biological databases represent an extraordinary collective volume of work. Diligently 70 built up over decades and comprised of many millions of contributions from the biomedical 71 research community, biological databases provide worldwide access to a massive number of 72 records (also known as entries) [1]. Starting from individual laboratories, genomes are 73 sequenced, assembled, annotated, and ultimately submitted to primary nucleotide databases such 74 as GenBank [2], ENA [3], and DDBJ [4] (collectively known as INSDC). Translations of those 75 nucleotide records, protein records, are deposited into central protein databases such as the 76 UniProt KnowledgeBase (UniProtKB) [5] and the Protein Data Bank [6]. Sequence records are 77 further accumulated into different databases for more specialised purposes: RFam [7] and PFam 78 [8] for RNA and protein families respectively, such as DictyBase [9] and PomBase [10] for 79 model organisms, ArrayExpress [11] and GEO [12] for gene expression profiles. These 80 databases are selected as examples; the list is not intended to be exhaustive. However, they are 81 representative of biological databases that have been named in the "golden set" of the 24th 82 Nucleic Acids Research database issue. The introduction of that issue highlights the databases 83 that "consistently served as authoritative, comprehens...
Background The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. Results Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. ‘macula,’ based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS , were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels. Conclusions These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation. Electronic supplementary material The online version of this article (10.1186/s12862-019-1387-2) contains supplementary material, which is available to authorized users.
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