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Background: Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results: The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions: The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity. [ABSTRACT FROM AUTHOR]

Pandoraviridae is a rapidly growing family of giant viruses, all of which have been isolated using laboratory strains of Acanthamoeba. The genomes of 10 distinct strains have been fully characterized, reaching up to 2.5 Mb in size. These double-stranded DNA genomes encode the largest of all known viral proteomes and are propagated in oblate virions that are among the largest ever described (1.2 μm long and 0.5 μm wide). The evolutionary origin of these atypical viruses is the object of numerous speculations. Applying the chaos game representation to the pandoravirus genome sequences, we discovered that the tetranucleotide (4-mer) “AGCT” is totally absent from the genomes of 2 strains (Pandoravirus dulcis and Pandoravirus quercus) and strongly underrepresented in others. Given the amazingly low probability of such an observation in the corresponding randomized sequences, we investigated its biological significance through a comprehensive study of the 4-mer compositions of all viral genomes. Our results indicate that AGCT was specifically eliminated during the evolution of the Pandoraviridae and that none of the previously proposed host-virus antagonistic relationships could explain this phenomenon. Unlike the three other families of giant viruses (Mimiviridae, Pithoviridae, and Molliviridae) infecting the same Acanthamoeba host, the pandoraviruses exhibit a puzzling genomic anomaly suggesting a highly specific DNA editing in response to a new kind of strong evolutionary pressure. IMPORTANCE Recent years have seen the discovery of several families of giant DNA viruses infecting the ubiquitous amoebozoa of the genus Acanthamoeba. With double-stranded DNA (dsDNA) genomes reaching 2.5 Mb in length packaged in oblate particles the size of a bacterium, the pandoraviruses are currently the most complex and largest viruses known. In addition to their spectacular dimensions, the pandoraviruses encode the largest proportion of proteins without homologs in other organisms, which is thought to result from a de novo gene creation process. While using comparative genomics to investigate the evolutionary forces responsible for the emergence of such an unusual giant virus family, we discovered a unique bias in the tetranucleotide composition of the pandoravirus genomes that can result only from an undescribed evolutionary process not encountered in any other microorganism. [ABSTRACT FROM AUTHOR]

The hexaploid species of Helianthus tuberosus is a potential source of resistance to several sunflower pathogens. But crossed with cultivated sunflower, it produces F1 hybrids which have low values of fertility or even full sterility. Pollen viability and meiotic features were studied in 17 populations of the species H. tuberosus and in F1 hybrids. Significant differences in pollen viability existed between populations (47.1- 98.8 %). In the 15 F1 hybrids, plant fertility ranged from 0 to 100 % per combination, while pollen viability ranged from 12.4 to 57.1 %. Meiosis was almost normal in the analyzed species, and irregular in the F1 hybrids. The highest percentage of meiocytes was with bivalents (85.9), but univalents (0.3 %) and multivalents (13.8 %) occurred as well. In metaphase and anaphase, the percentage of meiocytes with fast and lagging chromosomes was high. In anaphase, chromosome bridges were detected in 9.9 % of the meiocytes. [ABSTRACT FROM AUTHOR]

In this study, we sequenced the entire mitochondrial genome of Boer goat. The mitogenome was 16,639 bp in length, comprised of 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 putative control region. Almost all genes were encoded on the H-strand except theND6and eight tRNA genes. Most of the genes initiated with ATG, whereasND2, ND3andND5started with ATA. The total base composition of the mitogenome was 33.53% for A, 26.05% for C, 13.12% for T and 27.30% for G. These results provide a standard reference sequence for phylogenetic analyses among goats. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of the longsnout seahorseHippocampus reidiwas fisrt determined in this article. The total length ofH. reidimitogenome is 16,529 bp and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The gene order and composition ofH. reidiwere similar to those of most other vertebrates. The overall base composition ofH. reidiis 32.47% A, 29.41% T, 14.75% G and 23.37% C, with a slight A + T rich feature (61.88%). [ABSTRACT FROM AUTHOR]

Lantang pig is a native breed of Guangzhou Province in China. It is the first time that the complete mitochondrial genome sequence of Lantang pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,709 bp, which contains 2 ribosomal RNA genes, 22 tRNA genes, 13 PCGs and 1 conntrol region (D-loop region, Table 1). The total base composition of Lantang pig mitochondrial genome is 34.69% for A, 26.18% for C, 25.82% for T and 13.31% for G, in the order A>C>T>G. The complete mitochondrial genome of Lantang pig provides an important data in genetic mechanism and the evolution genomes. [ABSTRACT FROM AUTHOR]

In this study, the complete mitochondrial genome sequence of Diannan small-ear pig in Yunnan Province was firstly reported, which was determined through polymerase chain reaction (PCR) method. The total length of mitochondrial genome of Diannan small-ear pig was 16720 bp, including 34.77% A, 26.18% C, 25.81% T and 13.24% G, and in the order A > C > T > G. Mitochondrial genome contained a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. The mitochondrial genome of Diannan small-ear pig provides an important data set for the study on genetic mechanism. [ABSTRACT FROM AUTHOR]

Rongchang pig is one of the native breeds in Sichuan province in China. The total length of mitochondrial genome of Rongchang pig is 16,710 bp, including 34.67% A, 26.18% C, 25.82% T and 13.33% G, and in the order A > C > T > G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Rongchang pig. The mitochondrial genome of Rongchang pig subsequently provides an important information in genetic mechanism and the evolution genomes. [ABSTRACT FROM AUTHOR]

In the present study, the ear tissue of an adult Laiwu Black pig is from the Shandong province of China. The complete mitochondrial genome of Laiwu Black pig was determined by polymerase chain reaction (PCR). The complete mitochondrial genome is 16,710 bp, and it contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a control region (D-loop), with the genome organization and gene order being identical to that of the typical vertebrates. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of the Barbour’s seahorseHippocampus barbouriwas first determined in this paper. The total length ofH. barbourimitogenome is 16,526 bp, which consists of 13 protein-coding genes, 22 tRNA and 2 rRNA genes and 1 control region. The features of theH. barbourimitochondrial genome were similar to the typical vertebrates. The overall base composition ofH. barbouriis 32.68% A, 29.75% T, 22.91% C and 14.66% G, with an AT content of 62.43%. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome sequence of Qianshao spotted pig was first determined in this study. The mitogenome (16,700 bp) consists of 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the Qianshao spotted pig enriches data resource for further study in genetic mechanism. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome sequence of the pacific seahorse Hippocampus ingens was determined using long polymerase chain reactions. The total length of H. ingens mitogenome is 16,526 bp and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of H. ingens were similar to those of most other vertebrates. The overall base composition of H. ingens is 32.6% A, 29.3% T, 23.5% G and 14.6% C, with a slight A+T rich feature (61.9%). [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of the lined seahorseHippocampus erectuswas first determined in this article. The total length ofH. erectusmitogenome is 16,529 bp, which consists of 13 protein-coding genes, 22 tRNA and 2 rRNA genes and 1 control region. The features of theH. erectusmitochondrial genome were similar to the typical vertebrates. The overall base composition ofH. erectusis 31.8% A, 28.6% T, 24.3% C and 15.3% G, with a slight A + T rich feature (60.4%). [ABSTRACT FROM PUBLISHER]