RESUMO
The complete chloroplast genome (cpDNA) sequences of two cultivated species of Morus L. (Morus atropurpurea and Morus multicaulis) are reported and reconstructed in this study, and were compared with that of wild Morus mongolica. In M. atropurpurea, the circular genome is 159,113 bp in size and comprises two identical inverted repeat (IR) regions of 25,707 bp each, separated by a large single-copy (LSC) region of 87,824 bp and a small single-copy (SSC) region of 19,875 bp. The cpDNA sequence of M. multicaulis is longer than that of M. atropurpurea (159,154 bp), and consists of two IRs (25,678 bp), a LSC region (87,763 bp), and a SSC region (20,035 bp). Each cpDNA contains 112 unique genes including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes, with a GC content of 36.2%. There were 83 simple sequence repeats (SSRs) with mononucleotides being the most common (60) and di-, tri-, tetra-, and hexanucleotides appearing less frequently in M. atropurpurea. M. multicaulis contains 81 SSRs containing 63 mononucleotide repeats. The genes and SSRs identified in this study may enhance understanding of cpDNA evolution at both intra- and interspecific levels. MEGA 6.0 was used to construct a phylogenetic tree of 27 species, which revealed that M. atropurpurea and M. multicaulis are more related to their congeners than to others. The cpDNA of M. atropurpurea and M. multicaulis and its structural analysis are important for the chloroplast genome project, development of molecular markers for Morus species, and breeding of varieties.
Assuntos
DNA de Cloroplastos/genética , Genoma de Planta , Morus/crescimento & desenvolvimento , Morus/genética , Sequência de Bases , Mapeamento Cromossômico , Códon/genética , Genes de Plantas , Loci Gênicos , Funções Verossimilhança , Repetições de Microssatélites/genética , Filogenia , Especificidade da EspécieRESUMO
Nucleotide and codon usage are typically examined to investigate viral evolution. In this study, we analyzed the genetic information of 46 strains of classical swine fever virus (CSFV) RNA, nucleotide usage in the internal ribosome entry site (IRES), the nucleotide context surrounding the initiation codon, and synonymous codon usage in the translation initiation region. Phylogenetic analysis of the IRES element indicated that the genetic diversity of this element is generally similar to the phylogenetic clusters of CSFV genotypes. Nucleotides surrounding the initiation codon of CSFV RNA were generally more stable (ACAUGGCACAUGGAGUUG) compared to the internal AUG in the CSFV coding sequence. The second codon position after the initiation codon was generally selected to be GAG, which has lower tRNA abundance in pigs than its synonymous member (GAA). Regarding the synonymous codon usage bias in the CSFV translation initiation region, some codons showing low tRNA abundance in pigs are more frequently located in the translation initiation region than in the open reading frame of CSFV. Although CSFV, similarly to other RNA viruses, has a high mutation rate in nature, the regulatory features of nucleotide and synonymous codon usage of the IRES element, the nucleotide context surrounding the initiation codon and the translation initiation region in CSFV RNA have been 'branded' in the system of translation initiation to accommodate gene expression mediated by the cap-independent translation mechanism.
Assuntos
Vírus da Febre Suína Clássica/classificação , Vírus da Febre Suína Clássica/genética , RNA Viral/genética , Sequências Reguladoras de Ácido Ribonucleico , Animais , Vírus da Febre Suína Clássica/fisiologia , Códon de Iniciação , Evolução Molecular , Variação Genética , Filogenia , Biossíntese de Proteínas , RNA de Transferência/genética , Análise de Sequência de RNARESUMO
Adaptation in the overall codon usage pattern of West Nile virus (WNV) to that of two hosts was estimated based on the synonymous codon usage value (RSCU). Synonymous codon usage biases for the beginning coding sequence of this virus were also analyzed by calculating the usage fluctuation for each synonymous codon along the target region (the first 270 codon sites of the whole coding sequence of WNV). Adaptation of WNV to Anopheles gambiae regarding the overall codon usage revealed a mixture of synonymous codon usage patterns between this virus and its vector. Regarding the adaptation of WNV to its dead-end host and codon usage, although a mixture of overall codon usage patterns exists, the number of codons with reversed tendency codon usage is lower than that between the virus and its vector. In addition, some codons with low RSCU values for this virus are highly selected in the beginning translation region of WNV, while codons with low RSCU values in this region tend to pair with tRNAs present in low abundance in the host, suggesting that highly selected codons in a specific region in the beginning region of WNV are, to some degree, influenced by the corresponding low tRNA abundance of hosts to regulate the translation speed of the WNV polyprotein.
Assuntos
Códon , Fases de Leitura Aberta , RNA Viral , Vírus do Nilo Ocidental/genética , Interações Hospedeiro-Patógeno , RNA de TransferênciaRESUMO
To analyze the synonymous codon usage patterns of sequence regions flanking cleavage sites in the hepatitis A virus (HAV) polyprotein, the codon usage bias at codon positions and the synonymous codon usage in the target contexts of 30 virus strains were estimated by two simple methods that were based on the values for relative synonymous codon usage. In addition, the pattern of synonymous codon usage was compared between the genomic sequences in HAV and those of its human host. Our results indicated that HAV adopts a combination of coincidence and antagonism with the synonymous codon usage in humans. This characteristic may help HAV to efficiently use the translational machinery in its human host. We also observed that codon usage exhibited a strong bias in some specific positions in these contexts, and that the underrepresented synonymous codons, CUA for Leu, ACG for Thr, GUA for Val, and UCG for Ser, are preferentially used in these positions. These underrepresented synonymous codons likely play roles in regulating the rate of protein translation and influencing the secondary structure of the sequence regions flanking the cleavage sites.
Assuntos
Códon/genética , Vírus da Hepatite A/genética , Poliproteínas/genética , Proteólise , Proteínas Virais/genética , DNA Viral/química , DNA Viral/metabolismo , Genoma Humano , Genoma Viral , Vírus da Hepatite A/metabolismo , Humanos , Poliproteínas/metabolismo , Análise de Sequência de DNA , Proteínas Virais/metabolismoRESUMO
Peptidoglycan recognition protein 2 (PGLYRP-2), which belongs to the PGRP family, is the only member that has no direct bactericidal activity but has N-acetylmuramoyl-l-alanine amidase activity. This feature of PGLYRP-2 indicates that it may play an important role in eliminating the pathogen associated molecular pattern (PAMP), such as peptidoglycan (PGN), which can reduce leukocytes in blood and lower somatic cell count (SCC) in milk. To investigate whether the PGLYRP-2 gene is associated with mastitis and milk production traits in dairy cattle, the polymorphism of this gene was analyzed by PCR-RFLP in a population of 546 Chinese Holstein cows. A total of five single nucleotide polymorphism (SNP) loci were identified. The association analysis of a single SNP locus showed that the C+4867T locus was significantly associated (P < 0.05) with somatic cell score (SCS). Surprisingly, all loci were significantly associated (P < 0.01 or P < 0.05) with percentage of fat. Association analysis between combined genotypes and SCS and milk production traits indicated that H2H2 was associated with higher percentage of fat (P < 0.05). These findings demonstrated that SNPs in PGLYRP-2 gene were related to mastitis resistance and percentage of fat, and that H2H2 would be a useful genetic marker of combined genotypes for breeding of Chinese Holstein.