Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them.

Rice yellow mottle virus (RYMV), transmitted by chrysomelids, is one of the major viral pathogens that has devastated rice production in Sub-Saharan Africa. RYMV is a member of the genus Sobemoviruses in the family Solemoviridae and harbors a positive-sense single-stranded RNA (+ssRNA). Here, we used 50 RYMV strains, applying the codon usage bias (CUB). Both base content and relative synonymous codon usage (RSCU) analysis revealed that GC-ended codons were more frequently used in the genome of RYMV. Further low codon usage bias was observed from the effective number of codons (ENC) value. The neutrality plot analysis suggested the dominant factor of natural selection was involved in the structuring of CUB in RYMV. Based on RSCU values, the RYMV and its host relationship indicate that the RYMV develops codon usage patterns similar to its host. Generally, both natural selection and mutational pressure impact the codon usage pattern of the protein-coding genes in RYMV. This study is important because it characterized the codon usage pattern in the RYMV genomes and provided the necessary data for a basic evolutionary study on them. Additionally, we recommend that experiments such as whole genome sequencing (WGS) or dual RNA sequencing (DRS) should be considered in order to correlate these in-silico findings with viral diseases in the future.

Ulmus villosa Brandis ex Gamble, an economically and ecologically important forest tree, is native to the western Himalayas of Pakistan. The long pressure imposed by unsustainable utilization and market demands has resulted in the rapid decline of the U. villosa population in the wild. To date, very limited information on the genomic diversity of U. villosa is available and this can tremendously limit our understanding of distribution and future conservation of U. villosa. Therefore, the current study aimed to assess genetic diversity within U. villosa wild populations of the Hazara Division using four barcoding markers (i.e., rbcL, matK XF + 5R, matK 390F + 1326R and trnH-psbA). A total of six high quality sequences were obtained with rbcL, four with matK XF + 5R, four with matK 390F + 1326R, and fourteen with trnH-psbA. The sequenced regions contained insertions and deletions as well as several SNPs across the length of sequences, and PCR-based markers may be developed from these novel SNPs markers. The phylogenetic results supported the polyphyletic origin of the genus Ulmus, and the data indicated that multiple speciation events may have led to the evolution of U. villosa in this region. For deeper understanding of the origin and evolution of U. villosa, sequencing of the complete nuclear and chloroplast genomes will be pivotal. The results herein provide novel insights into the genomic diversity as well as phylogenetic relationships of U. villosa with other species, and may facilitate both in situ and ex situ conservation efforts for this endangered species.