The porcine deltacoronavirus (PDCoV) is a newly discovered pig enteric coronavirus that can infect cells from various species. In Haiti, PDCoV infections in children with acute undifferentiated febrile fever were recently reported. Considering the great potential of inter-species transmission of PDCoV, we performed a comprehensive analysis of codon usage patterns and host adaptation profiles of 54 representative PDCoV strains with the spike (S) gene. Phylogenetic analysis of the PDCoV S gene indicates that the PDCoV strains can be divided into five genogroups. We found a certain codon usage bias existed in the S gene, in which the synonymous codons are often ended with U or A. Heat map analysis revealed that all the PDCoV strains shared a similar codon usage trend. The PDCoV S gene with a dN/dS ratio lower than 1 reveals a negative selection on the PDCoV S gene. Neutrality analysis showed that natural selection is the dominant force in shaping the codon usage bias of the PDCoV S gene. Unexpectedly, host adaptation analysis reveals a higher adaptation level of PDCoV to Homo sapiens and Gallus gallus than to Sus scrofa. Compared to the USA lineage, the PDCoV strains in the Early China lineage and Thailand lineage were less adapted to their hosts, which indicates that the evolutionary process plays an important role in the adaptation ability of PDCoV. These findings of this study add to our understanding of PDCoV's evolution, adaptability, and inter-species transmission.
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Mol Cell
December 2024
Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA. Electronic address:
The efficacy of antibody responses is inherently linked to paratope diversity, as generated through V(D)J recombination and somatic hypermutation. Despite this, it is unclear how genetic diversification mechanisms evolved alongside codon optimality and affect antibody expression. Here, we analyze germline immunoglobulin (IG) genes, natural V(D)J repertoires, serum IgG, and monoclonal antibody (mAb) expression through the lens of codon optimality.
View Article and Find Full Text PDFMol Genet Genomics
December 2024
Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
The brown pencilfish, Nannostomus eques is a lebiasinid harvested for ornamental purposes; however, its complete mitochondrial genome sequence is still unknown. To enrich the molecular genetic information pertaining to Nannostomus, we present here the first report of the complete mitochondrial genome sequence of Nannostomus eques and compare it with Nannostomus beckfordi. The total lengths of the N.
View Article and Find Full Text PDFEcol Evol
December 2024
Anhui Province Key Laboratory of Integrated Pest Management on Crops, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection Anhui Agricultural University Hefei Anhui China.
Previous studies on the gene order and composition of leafhopper mitochondrial genomes have revealed a high level of conservation in overall genome structure. Some members of Deltocephalinae, the largest subfamily, exhibit tRNA gene rearrangements; however, few mitogenomes have been sequenced in this group and the degree of structural variation within tribes remains unclear. In this study, we sequenced the complete mitogenomes of 14 species belonging to four genera of tribe Deltocephalini from China and compared them with the two previously reported mitogenomes for this tribe.
View Article and Find Full Text PDFPLoS Genet
December 2024
Earlham Institute, Norwich Research Park, Norwich, United Kingdom.
The translation of nucleotide sequences into amino acid sequences, governed by the genetic code, is one of the most conserved features of molecular biology. The standard genetic code, which uses 61 sense codons to encode one of the 20 standard amino acids and 3 stop codons (UAA, UAG, and UGA) to terminate translation, is used by most extant organisms. The protistan phylum Ciliophora (the 'ciliates') are the most prominent exception to this norm, exhibiting the grfeatest diversity of nuclear genetic code variants and evidence of repeated changes in the code.
View Article and Find Full Text PDFTheory Biosci
December 2024
Institute for Mathematical Biology Faculty of Computer Sciences, Mannheim University of Applied Sciences, 68163, Mannheim, Germany.
Circular codes, which are considered as putative remnants of primaeval comma-free codes, have recently become a focal point of research. These codes constitute a secondary type of genetic code, primarily tasked with detecting and preserving the normal reading frame within protein-coding sequences. The identification of a universal code present across various species has sparked numerous theoretical and experimental inquiries.
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