Codon Usage Analysis Research Articles

Genetic and Structural Factors Contributing to the Dominance and Persistence of Goose Astrovirus Type 2

: Goose astrovirus (GoAstV) has emerged as a significant pathogen affecting the goose industry in China, with GoAstV-2 becoming the dominant genotype since 2017. This study explores the genetic and structural factors underlying the prevalence of GoAstV-2, focusing on codon usage bias, spike protein variability, and structural stability. Phylogenetic and effective population size analyses revealed that GoAstV-2 experienced rapid expansion between 2017 and 2018, followed by population stabilization. Codon usage analysis indicated that GoAstV-2 exhibited a weaker codon usage bias compared to GoAstV-1, suggesting greater flexibility in synonymous codon usage and potentially enhanced adaptability across host environments. Additionally, GoAstV-2's lower codon adaptation index values point to a divergence from the host’s optimal codon usage, which may reduce competition with host tRNA pools and facilitate viral replication. The spike protein of GoAstV-2 demonstrated significantly lower variability than GoAstV-1, as shown by Shannon entropy analysis, indicating greater structural stability. This stability may reduce the need for frequent mutations, allowing GoAstV-2 to persist in host populations without undergoing constant evolution. The lower antigenic variability likely decreases immune-driven selective pressure, contributing to the viral sustained transmission and long-term persistence. These findings provide new insights into the evolutionary advantages of GoAstV-2 and its epidemiological success, which could inform future control strategies aimed at mitigating its impact on poultry populations.

Mitochondrial Genome Characteristics Reveal Evolution of Danxiaorchis yangii and Phylogenetic Relationships

Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species’ adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids.

Compare Analysis of Codon Usage Bias of Nuclear Genome in Eight Sapindaceae Species.

Codon usage bias (CUB) refers to the different frequencies with which various codons are utilized within a genome. Examining CUB is essential for understanding genome structure, function, and evolution. However, little was known about codon usage patterns and the factors influencing the nuclear genomes of eight ecologically significant Sapindaceae species widely utilized for food and medicine. In this study, an analysis of nucleotide composition revealed a higher A/T content and showed a preference for A/T at the third codon position in the eight species of Sapindaceae. A correspondence analysis of relative synonymous codon usage explained only part of the variation, suggesting that not only natural selection but also various other factors contribute to selective constraints on codon bias in the nuclear genomes of the eight Sapindaceae species. Additionally, ENC-GC3 plot, PR2-Bias, and neutrality plot analyses indicated that natural selection exerted a greater influence than mutation pressure across these eight species. Among the eight Sapindaceae species, 16 to 26 optimal codons were identified, with two common high-frequency codons: AGA (encoding Arg) and GCU (encoding Ala). The clustering heat map, which included the 8 Sapindaceae species and 13 other species, revealed two distinct clusters corresponding to monocots and dicots. This finding suggested that CUB analysis was particularly effective in elucidating evolutionary relationships at the family level. Collectively, our results emphasized the distinct codon usage characteristics and unique evolutionary traits of the eight Sapindaceae species.

Identification of CD8+ Immunogenic Peptides for Vaccine Design against Nipah Virus in Humans

Background: Nipah virus is a pathogenic virus of ruinous zoonotic potential with inflated rate of mortality in humans. Methods: Considering the emerging threat of this pandemic virus, the present investigation amid to design vaccine by using the bioinformatics tools such as host and virus codon usage analysis, CD8+ peptide prediction, immunogenicity/allergenicity/toxicity, MHC-I allele binding prediction and subsequent population coverage and MHC-I-peptide docking analysis. Results: In this study (conducted in 2022 at School of Biotechnology, Katra, India), a set of 11 peptides of the structural proteins of Nipah Virus were predicted and recognized by the set of MHC-I alleles that are expressed in 92% of the global human population. Conclusion: The strong interactions between these peptides and the MHC-I protein suggest them as strong peptide candidates for the development of vaccine against Nipah Virus.

Characterization of the Complete Chloroplast Genomes and Phylogenetic Analysis of Sapotaceae

The Sapotaceae family comprises 65–70 genera and over 1250 species, holding significant ecological and economic value. Although previous studies have made some progress in the phylogenetic relationships and classification of Sapotaceae, many issues remain unresolved and require further in-depth research. In this study, we sequenced and assembled the complete chloroplast genomes of 21 plants from 11 genera of Sapotaceae, conducted a comparative genomic analysis, and performed a phylogenetic analysis by incorporating 16 previously published chloroplast genomes of Sapotaceae. The results showed that the chloroplast genome sizes in 21 plants of Sapotaceae range between 157,920 bp and 160,130 bp, exhibiting the typical quadripartite structure. Each genome contains 84–85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, while the ndhF gene is absent in Pouteria campechiana and Pouteria sapota. The relative synonymous codon usage (RSCU) analysis showed that isoleucine (Ile) is the most commonly used, while the codon for methionine (Met) is the least utilized. Additionally, five highly variable regions (petA-psbJ, psbI-trnS-GGA, rpl2_2-psbA, rps19-rpl2_2, and ycf4-cemA) and two coding sequences, ycf1 and matK, were identified as candidate molecular markers for species differentiation and a phylogenetic analysis within the Sapotaceae family. Phylogenetic trees were reconstructed using complete chloroplast genome sequences and analyzed using ML and BI methods, which revealed that the Sapotaceae family is divided into three distinct clades, each receiving strong statistical support (BS = 100, PP = 1). The intergeneric analysis revealed that Madhuca and Palaquium are sister groups (BS = 91, PP = 1), as are Gambeya and Chrysophyllum (BS = 91, PP = 1). Pouteria and Chrysophyllum are among the larger groups in the Sapotaceae family but the traditional classification boundaries of these genera are unstable and unfeasible, as the current genus boundaries fail to support their natural evolutionary relationships. In the phylogenetic tree, Eberhardtia aurata is placed on a separate branch. The morphological classification system shows that E. aurata has rust-colored pubescence on its branches, abaxial leaf surfaces, petioles, and other areas, which clearly distinguishes it from other genera. This study provides valuable insights into advancing phylogenetic research, population genetics, molecular breeding, and conservation strategies by comparing chloroplast genome structures and characteristics and constructing phylogenetic trees.

Complete chloroplast genome characterization of three Plagiomnium species and the phylogeny of family Mniaceae.

The taxonomic concepts and phylogenetic relations among genera of the family Mniaceae have given rise to much controversy in recent years, including Mnium, Plagiomnium, and Pohlia. Chloroplast genome study of these genera will be helpful to reflect the fact of this relationship. In this study, we sequenced three species in the Plagiomnium genus using an Illumina HiSeq 4000 platform. The complete chloroplast genomes of P. rostratum, P. succulentum and P. vesicatum were 125,196bp, 124,689bp, and 124,663bp in length, which all contained a quadripartite structure including two copies of the invert repeats (IR, 10,120bp, 9,818bp, and 9,665bp), one large single copy region (LSC, 86,395bp, 86,299bp, and 86,532bp), and one single copy region (SSC, 18,561bp, 18,754bp, and 18,801bp). The overall GC contents were 29.8%, 30.5%, and 30.5% respectively. The simple sequence repeats (SSRs) were detected in conjunction with Plagiomnium acutum, with variable sites genes observed: rpoC2, ycf1, and ycf2. Combined with the other three sequences published in Mniaceae, analyses of codon usage, repeats sequences, GC contents, and gene features revealed similarities among the seven species in Mniaceae. The trend of nucleotide diversity (Pi) in the seven complete chloroplast genomes showed Pi > 0.056: trnI-rpl23, petG-petL-psbE, trnK-chlB, trnG-trnR-atpA, rpoB-trnC-ycf66, ndhB, trnN-ndhF, and rps15-ycf1. We confirmed the phylogenetic relationships that Plagiomnium genus is a sister group with Mnium, while the Pohlia genus is not a monophyletic group. Phylogenetic analyses corroborated the monophyly of Mniaceae and supported the transfer of the Pohlia genus into Mniaceae.

Comparative chloroplast genome analysis of two Desmodesmus species reveals genome diversity within Scenedesmaceae (Sphaeropleales, Chlorophyceae)

Desmodesmus (Sphaeropleales, Chlorophyceae) is a genus of freshwater green algae widely distributed in aquatic ecosystems and known for its potential in biotechnology and bioremediation. We present the complete chloroplast genome sequences of two Desmodesmus species, D. hystrix and D. perforatus . Comparative analysis revealed significant differences in their quadripartite structures, particularly in the lengths of the small single copy regions. We observed variations in G + C content across genomic regions, with inverted repeat regions showing a higher G + C content. Microsatellite analysis revealed that A/T mononucleotides were the most abundant type, while dispersed repeat analysis suggested a potential link to expansion of the single-copy region in D. perforatus. Gene annotation, codon usage analysis, and comparison of genome rearrangement highlighted both similarities and differences between the species. Nucleotide diversity analysis revealed higher variability in intergenic regions than in coding regions, with IR regions displaying relative conservation. Comparative analyses of genomes and IR border arrangements demonstrated that the Desmodesmus species exhibit substantial differences in genome structure and gene arrangement among Scenedesmaceae. Phylogenetic analysis, based on 51 single-copy genes from 34 species of Sphaeropleales provided additional information about phylogenetic relationships within Sphaeropleales. These findings contribute to our understanding of comparative plastid genomics in green algae.

Complete Chloroplast Genomes and Phylogenetic Analysis of Woody Climbing Genus Phanera (Leguminosae).

Phanera Lour., a genus in the subfamily Cercidoideae of the family Leguminosae, is characterized by woody liana habit, tendrils, and distinctive bilobate or bifoliolate leaves. The genus holds important medicinal value and constitutes a complex group characterized by morphological diversity and unstable taxonomic boundaries. However, limited information on the chloroplast genomes of this genus currently available constrains our understanding of its species diversity. Hence, it is necessary to obtain more chloroplast genome information to uncover the genetic characteristics of this genus. We collected and assembled the complete chloroplast genomes of nine representative Phanera plants, including Phanera erythropoda, Phanera vahlii, Phanera aureifolia, Phanera bidentata, Phanera japonica, Phanera saigonensis, Phanera championii, Phanera yunnanensis, and Phanera apertilobata. We then conducted a comparative analysis of these genomes and constructed phylogenetic trees. These species are each characterized by a typical quadripartite structure. A total of 130-135 genes were annotated, and the GC content ranged from 39.25-42.58%. Codon usage analysis indicated that codons encoding alanine were dominant. We found 82-126 simple sequence repeats, along with 5448 dispersed repeats, mostly in the form of forward repeats. Phylogenetic analysis revealed that 16 Phanera species form a well-supported monophyletic group, suggesting a possible monophyletic genus. Furthermore, 10 hypervariable regions were detected for identification and evolutionary studies. We focused on comparing chloroplast genome characteristics among nine Phanera species and conducted phylogenetic analyses, laying the foundation for further phylogenetic research and species identification of Phanera.

Kazakhstan tulips: comparative analysis of complete chloroplast genomes of four local and endangered species of the genus Tulipa L.

Species of Tulipa are important ornamental plants used for horticultural purposes in various countries, across Asia, Europe, and North Africa. The present study is the first report on typical features of the complete chloroplast genome sequence of four local and endangered species including T. alberti, T. kaufmanniana, T. greigii, and T. dubia from Kazakhstan using Illumina sequencing technology. The comparative analyses revealed that the complete genomes of four species were highly conserved in terms of total genome size (152. 006 bp - 152. 382 bp), including a pair of inverted repeat regions (26. 330 bp - 26. 371 bp), separated by a large single copy region (82.169 bp - 82,378 bp) and a small copy region (17.172 bp -17.260 bp). Total GC content (36.58-36.62 %), gene number (131), and intron length (540 bp - 2620 bp) of 28 genes. The complete genomes of four species showed nucleotide diversity (π =0,003257). The total number of SSR loci was 159 in T. alberti, 158 in T. kaufmanniana, 174 in T. greigii, and 163 in T. dubia. The result indicated that ten CDS genes, namely rpoC2, cemA, rbcL, rpl36, psbH, rps3, rpl22, ndhF, ycf1, and matK, with effective polymorphic simple sequence repeats (SSRs), high sequence variability (SV) ranging from 2.581 to 6.102, and high nucleotide diversity (Pi) of these loci ranging from 0,004 to 0,010. For all intergenic regions longer than 150 bp, twenty one most variable regions were found with high sequence variability (SV) ranging from 4,848 to 11,862 and high nucleotide diversity (Pi) ranging from 0,01599 to 0,01839. Relative synonymous codon usage (RSCU) analysis was used to identify overrepresented and underrepresented codons for each amino acid. Based on the phylogenic analysis, the sequences clustered into four major groups, reflecting distinct evolutionary lineages corresponding to the subgenera Eriostemons, Tulipa, and Orithyia. Notably, T. greigii was distinctively grouped with species from Orithyia and Eriostemons rather than with other Tulipa species, suggesting a unique evolutionary history potentially shaped by geographical isolation or specific ecological pressures. The complete chloroplast genome of the four Tulipa species provides fundamental information for future research studies, even for designing the high number of available molecular markers.

Complete Mitogenomes of Xinjiang Hares and Their Selective Pressure Considerations.

Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base content and bias analysis, tRNA analysis, phylogenetic analysis, and amino acid sequence analysis of the annotated genes to understand their characteristics and phylogenetic relationship. Their mitogenomes are circular molecules (from 16,691 to 17,598 bp) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region, which are similar with other Lepus spp. worldwide. The relative synonymous codon usage analysis revealed that the adaptation of Lepus yarkandensis to its unique arid and hot environment might be associated with synthesizing amino acids like alanine, leucine, serine, arginine, and isoleucine and the terminator caused by the different usage of codons. Further, we utilized the MEME model and identified two positive selection genes (ND4, ND5) in Lepus tibetanus pamirensis and one (ND5) in L. yarkandensis that might be important to their adaptation to the plateau and dry and hot basin environments, respectively. Meanwhile, Lepus tolai lehmanni and Lepus timidus may have evolved different adaptive mechanisms for the same cold environment. This study explored the evolutionary dynamics of Xinjiang hares' mitochondrial genomes, providing significant support for future research into their adaptation mechanisms in extreme environments.

Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis

BackgroundHabenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.ResultsWe sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259–155,269 bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.ConclusionsThe results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.

Assembly and comparative analysis of the multichromosomal mitochondrial genome of globally endangered seagrass Halophila beccarii

BackgroundHalophila beccarii is one of the oldest two generations of seagrass plants and one of the 10 species of seagrass currently at risk of extinction worldwide. Therefore, how to effectively protect the H. beccarii resources from extinction is a huge challenge. Molecular biology research can provide a scientific basis for species conservation. So far, there has been no detailed analysis of the mitochondrial genome of the genus Halophila.ResultsThe mitochondrial genome of H. beccarii was assembled into 28 circular chromosomes, ranging in length from 41,738 bp to 104,744 bp, with a total length of 1,964,072 bp and a GC content of 46.71%. It contains 39 genes, including 26 protein coding genes, 10 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 850 dispersed repeats, 1,205 simple repeats, 61 tandem repeats, and 120 RNA editing sites. Analysis of codon usage indicates that codons ending in A/U are preferred. Gene migration between the mitochondrial genome and the chloroplast genome was observed through homologous fragment detection. In addition, Ka/Ks analysis showed that most protein coding genes in the mitochondrial genome experienced negative selection, while only the nad3 gene experienced potential positive selection in most Alismatales. Nucleotide polymorphism analysis revealed variations in each gene, with rpl10 being the most significant. In addition, comparative analysis shows that the GC content is conserved, but there are significant differences in the size and structure of mitochondrial genomes among different species of Alismatales. The phylogenetic analysis based on the mitochondrial genome reflects the exact evolutionary and taxonomic status of H. beccarii.ConclusionIn this study, we sequenced and annotated the mitochondrial genome of H. beccarii, and compared it with the mitochondrial genomes of other plants in Alismatales. Our findings enrich the mitogenome database of seagrass plants and highlight the potential for mitochondrial genes to help decipher plant evolutionary history.

Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae).

To elucidate phylogenetic relationships within the leafhopper's subfamily Megophthalminae (Hemiptera: Cicadellidae), mitogenomes of 12 species of the subfamily were sequenced and assembled. These were added to the mitogenomes of the eight other species that are currently available. Mitogenome size ranged from 15,193 bp in Onukigallia onukii (Matsumura, 1912) to 15,986 bp in Multinervis guangxiensis (Li and Li, 2013), they all contained 37 genes, and gene order was similar to that in other leafhoppers. Nucleotide composition analysis showed that the AT content was higher than that of GC, and the protein-coding genes usually ended with A/T at the 3rd codon position. The Ka/Ks ratio showed that the CYTB gene has the slowest evolutionary rate, while ND4 is the gene with the fastest evolutionary rate. Relative synonymous codon usage analysis revealed the most frequently used codon was UUA (L), followed by CGA (R), and the least frequently used codon was CCG (P). Parity plot and neutrality plot analyses showed that the codon usage bias of mitochondrial genes was influenced by natural selection and mutation pressure. However, natural selection plays a major role, while the effect of mutation pressure was small. Effective number of codons values were 40.15-49.17, which represented relatively low codon bias. Phylogenetic analyses based on three datasets (AA, 13PCG, 13PCG_2rRNA) using two methods (maximum likelihood and Bayesian inference). In the obtained topology, the Megophthalminae species were clustered into a monophyletic group. In conclusion, our results clarify structural modules of the mitochondrial genes and confirm the monophyly of Megophthalminae within Cicadellidae.

Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.

Human papillomavirus type 51 (HPV-51) is associated with various cancers, including cervical cancer. Examining the codon usage bias of the organism can offer valuable insights into its evolutionary patterns and its relationship with the host. This study comprehensively analyzed codon usage bias in HPV-51 by examining 64 complete genome sequences sourced from the NCBI GenBank database. Our analysis revealed no noteworthy preference for codon usage in HPV-51 overall. However, there was a noticeable bias towards A/T-ending codons, accompanied by GC3s below 32%. Dinucleotide frequency analysis revealed reduced frequencies for ApA, CpG, and TpC dinucleotides, while CpA and TpG dinucleotides were more frequent than others. Relative Synonymous Codon Usage analysis revealed 30 favored codons, primarily concluding with A/T nucleotides. Further analysis using Parity Rule 2, Effective Number of Codons plot, and neutrality plot indicated a balance between mutational pressure and natural selection, with natural selection being the primary force shaping codon usage bias. The Isoacceptor tRNA Pool analysis indicates that HPV-51 has a higher translation efficiency within the human cellular translational system. Moreover, the Codon Adaptation Index and Relative Codon Deoptimization Index analyses suggested a moderate adaptation of HPV-51 to human codon preferences. Our discoveries offer valuable perspectives on how HPV-51 evolves and uses genetic codes, contributing to a deeper comprehension of its endurance and disease-causing potential.

Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India.

Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.

Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation

BackgroundThe Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.MethodsHere, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.ResultsThe mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.ConclusionsThis study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.

Complete chloroplast genomes of Desmidorchis penicillata (Deflers) plowes and Desmidorchis retrospiciens Ehrenb.: comparative and phylogenetic analyses among subtribe Stapeliinae (Ceropegieae, Asclepiadoideae, Apocynaceae)

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part of the taxonomically challenging genus Desmidorchis, are well‐known for their ecological resilience and medicinal significance. This study sequences the first complete chloroplast genomes of these species, shedding light on their genomic characteristics and evolutionary relationships. The circular genomes of D. penicillata (161 776 bp) and D. retrospiciens (162 277 bp) display a quadripartite structure typical of Angiosperms. Gene content, order, and GC content are consistent, featuring 114 unique genes, including 80 protein‐coding, 30 transfer RNAs, and four ribosomal RNAs genes. Codon usage analysis underscores A/U‐rich preferences, while RNA editing sites, predominantly in ndhB and ndhD genes, suggest post‐transcriptional modifications. Analysis of long repeated sequences reveals a predominance of forward and palindromic repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are abundant, with high presence of mononucleotide, offering potential molecular markers. Comparative analysis with their relatives in subtribe Stapeliinae identifies mutational hotspots such as ycf1, ndhF, trnG(GCC)‐trnfM(CGA) and ndhG‐ndhI that could be potential DNA barcoding markers. The inverted repeat (IR) boundaries analysis revealed an expansion of IR on the small single copy region, leading to the formation of a pseudogene. Overall, substitution rate analysis indicated purifying selection, with a few genes (rpl22, clpP and rps11) showing signatures of positive selection. Additionally, the phylogenetic analysis positioned Desmidorchis within the Stapeliinae clade and strongly supported the sister relationship between D. penicillata and D. retrospiciens. This study provides comprehensive molecular data for future research in Desmidorchis.

Codon Bias of the DDR1 Gene and Transcription Factor EHF in Multiple Species.

Milk production is an essential economic trait in cattle, and understanding the genetic regulation of this trait can enhance breeding strategies. The discoidin domain receptor 1 (DDR1) gene has been identified as a key candidate gene that influences milk production, and ETS homologous factor (EHF) is recognized as a critical transcription factor that regulates DDR1 expression. Codon usage bias, which affects gene expression and protein function, has not been fully explored in cattle. This study aims to examine the codon usage bias of DDR1 and EHF transcription factors to understand their roles in dairy production traits. Data from 24 species revealed that both DDR1 and EHF predominantly used G/C-ending codons, with the GC3 content averaging 75.49% for DDR1 and 61.72% for EHF. Synonymous codon usage analysis identified high-frequency codons for both DDR1 and EHF, with 17 codons common to both genes. Correlation analysis indicated a negative relationship between the effective number of codons and codon adaptation index for both DDR1 and EHF. Phylogenetic and clustering analyses revealed similar codon usage patterns among closely related species. These findings suggest that EHF plays a crucial role in regulating DDR1 expression, offering new insights into genetically regulating milk production in cattle.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study.

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

Limited Variation in Codon Usage across Mitochondrial Genomes of Non-Biting Midges (Diptera: Chironomidae).

The codon usage patterns of mitochondrial genomes offer insights into the evolutionary and phylogenetic studies of species. Codon usage analysis has been conducted in a few Chironomidae species, and the codon usage patterns in other species remain ambiguous. We aim to reveal the codon usage differences in the mitochondrial genomes across this family. We sequenced the first mitochondrial genome of the genus Conchapelopia and the third mitochondrial genome of the subfamily Tanypodinae. Then, we analyzed its relative synonymous codon usage and effective number of codons with registered mitochondrial genomes from 28 other genera. The results indicated that there was limited variation in codon usage across five subfamilies, Chironominae, Orthocladiinae, Diamesinae, Prodiamesinae and Tanypodinae. While Parochlus steinenii from Podonominae presented a weaker codon bias, P. steinenii possessed the most genes experiencing natural selection. Additionally, ND1, ND2 and ND3 were found to be the most frequently selected genes across all species. Our findings contribute to further understanding the evolutionary and phylogenetic relationships of Chironomidae.