SIX6 Shows High Divergence in Fusarium oxysporum f. sp. cubense TR4

Secreted fungal effector proteins and their host targets are good examples to understand the mechanism of host-pathogen co-evolution with genes involved in the interaction undergoing positive selection. SIX genes (secreted in xylem) are obtained via horizontal transfer and can be found within the formae speciales of Fusarium oxysporum. SIX6 and SIX9 of F. oxysporum f. spp. cubense (Foc) are predicted to play a role as effectors. However, their involvement in the pathogenicity of Foc in banana plants has not been determined yet. In the susceptible banana cultivar, we found that the SIX6 and SIX9 genes of Foc TR4 were highly expressed in roots, but not in corms or leaves. The host, however, expressed the pathogenesis-related (PR) genes, PR-1 and PR-3, in corms earlier than in the roots. Phylogenetic analysis on SIX6 and SIX9 genes of F. oxysporum has revealed the separation of SIX6 and SIX9 of Foc from other formae speciales. This leads to detecting genes under positive selection using the ratio nonsynonymous to synonymous substitution rates (Ka/Ks). SIX6 of Foc showed an increase in diversity, but insufficient to drive positive selection. Conversely, SIX9 of Foc showed no divergence in the dN/dS ratio distribution, indicating purifying selection. © 2021 Friends Science Publishers

Epidemiology, Genetic Characterization, and Evolution of Hunnivirus Carried by Rattus norvegicus and Rattus tanezumi: The First Epidemiological Evidence from Southern China

Hunnivirus is a novel member of the family Picornaviridae. A single species, Hunnivirus A, is currently described. However, there is limited information on the identification of Hunnivirus to date, and thereby the circulation of Hunnivirus is not fully understood. Thus, the objective of this study was to investigate the prevalence, genomic characteristics, and evolution of rat hunnivirus in southern China. A total of 404 fecal samples were subjected to detection of Hunnivirus from urban rats (Rattus norvegicus and Rattus tanezumi) using PCR assay based on specific primers targeted to partial 3D regions, with the prevalence of 17.8% in Rattus norvegicus and 15.6% in Rattus tanezumi. An almost full-length rat hunnivirus sequence (RatHuV/YY12/CHN) and the genome structure were acquired in the present study. Phylogenetic analysis of the P1 coding regions suggested the RatHuV/YY12/CHN sequence was found to be within the genotype of Hunnivirus A4. The negative selection was further identified based on analysis of non-synonymous to synonymous substitution rates. The present findings suggest that hunniviruses are common in urban rats. Further research is needed for increased surveillance and awareness of potential risks to human health.

Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae)

Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary timeline of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In the present study we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86–93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison to functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46-60 MYA in the lineage leading to modern true toads, a timeline that coincides with the rise of the family Bufonidae.

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

BackgroundFinger millet (Eleusine coracana2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome forE. indicaexisted. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs.ResultsWe produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within theEleusinegenus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A, 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes.ConclusionThe evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

ksrates: positioning whole-genome duplications relative to speciation events using rate-adjusted mixed paralog–ortholog KS distributions

Summary: To position ancient whole-genome duplication (WGD) events with respect to speciation events in a phylogeny, the KS values of WGD paralog pairs in a species of interest are often compared with the KS values of ortholog pairs between this species and other species. However, if the lineages involved exhibit different substitution rates, direct comparison of paralog and ortholog KS estimates can be misleading and result in phylogenetic misinterpretation of WGD signatures. Here we present ksrates, a user-friendly command-line tool to compare paralog and ortholog KS distributions derived from genomic or transcriptomic sequences. ksrates estimates differences in synonymous substitution rates among the lineages involved and generates an adjusted mixed plot of paralog and ortholog KS distributions that allows to assess the relative phylogenetic positioning of presumed WGD and speciation events. Availability and implementation: ksrates is open-source software implemented in Python 3 and as a Nextflow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https://github.com/VIB-PSB/ksrates.

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes.Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of transcript counts within the Circadian Rhythm Pathway suggests a possible A subgenomic preference. Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

Comparative Genomic Analyses Reveal a Specific Mutation Pattern Between Human Coronavirus SARS-CoV-2 and Bat-CoV RaTG13

BackgroundThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, rapidly grew into a global pandemic. How SARS-CoV-2 evolved remains unclear.MethodsWe performed a comprehensive analysis using the available genomes of SARS-CoV-2 and its closely related coronaviruses.ResultsThe ratio of nucleotide substitutions to amino acid substitutions of the spike gene (9.07) between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 was markedly higher than that between other coronaviruses (range, 1.29–4.81); the ratio of non-synonymous to synonymous substitution rates (dN/dS) between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 was the lowest among all the performed comparisons, suggesting evolution under stringent selective pressure. Notably, the relative proportion of the T:C transition was markedly higher between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 than between other compared coronaviruses. Codon usage is similar across these coronaviruses and is unlikely to explain the increased number of synonymous mutations. Moreover, some sites of the spike protein might be subjected to positive selection.ConclusionsOur results showed an increased proportion of synonymous substitutions and the T:C transition between SARS-CoV-2 and RaTG13. Further investigation of the mutation pattern mechanism would contribute to understanding viral pathogenicity and its adaptation to hosts.

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of expression within the circadian rhythm pathway suggests A subgenomic preference. Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.