scholarly journals Genome Assemblies of the Warthog and Kenyan Domestic Pig Provide Insights into Suidae Evolution and Candidate Genes for African Swine Fever Tolerance

2021 ◽  
Author(s):  
Wen Feng ◽  
Lei Zhou ◽  
Pengju Zhao ◽  
Heng Du ◽  
Chenguang Diao ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Resistance ◽  
African Swine Fever ◽  
Gene Families ◽  
Specific Gene ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Domestic Pig ◽  
Phacochoerus Africanus ◽  
Contraction And Expansion

As warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understanding the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthog's genome to adapt the environment. Importantly, the analysis of presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. The Combining with large scale sequencing data of 123 pigs from all over world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.

scholarly journals Genome Sequences of Three African Swine Fever Viruses of Genotypes IV and XX from Zaire and South Africa, Isolated from a Domestic Pig (Sus scrofa domesticus), a Warthog (Phacochoerus africanus), and a European Wild Boar (Sus scrofa)

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
S. Ndlovu ◽  
A.-L. Williamson ◽  
L. Heath ◽  
O. Carulei
Keyword(s):  
South Africa ◽  
Wild Boar ◽  
Sus Scrofa ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Genome Sequences ◽  
Domestic Pig ◽  
European Wild Boar ◽  
Sus Scrofa Domesticus ◽  
Phacochoerus Africanus

ABSTRACT We report here the genome sequences of three African swine fever virus isolates obtained from a domestic pig (Zaire [Zaire]), a warthog (RSA/W1/1999 [South Africa]), and a European wild boar (RSA/2/2004 [South Africa]) belonging to genotypes IV, XX, and XX, respectively. This report increases the number of genotype XX, wild boar, and warthog reference sequences available.

scholarly journals Comparative transcriptomic analysis reveals conserved transcriptional programs underpinning organogenesis and reproduction in land plants

2020 ◽  
Author(s):  
Irene Julca ◽  
Camilla Ferrari ◽  
María Flores-Tornero ◽  
Sebastian Proost ◽  
Ann-Cathrin Lindner ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Families ◽  
Male Reproduction ◽  
Land Plants ◽  
Easy Access ◽  
Specific Gene ◽  
Male Gametes ◽  
Organ Specific

AbstractThe evolution of plant organs, including leaves, stems, roots, and flowers, mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. Furthermore, the fertilization products of angiosperms, seeds serve as the basis for most of our food. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes, and the development of novel regulatory programs. However, our knowledge of these events is limited, as no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we have generated gene expression atlases for various organs and gametes of 10 plant species comprising bryophytes, vascular plants, gymnosperms, and flowering plants. Comparative analysis of the atlases identified hundreds of organ- and gamete-specific gene families and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, the appearance of organ-specific gene families does not coincide with the corresponding organ’s appearance, suggesting that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, suggesting that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function. To provide easy access to the expression atlases and these comparative analyses, we provide an online database, www.evorepro.plant.tools, that allows the exploration of expression profiles, organ-specific genes, phylogenetic trees, co-expression networks, and others.

scholarly journals Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sofia A. Bengoa Luoni ◽  
Alberto Cenci ◽  
Sebastian Moschen ◽  
Salvador Nicosia ◽  
Laura M. Radonic ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Leaf Senescence ◽  
Large Scale ◽  
Gene Families ◽  
Orthologous Group ◽  
Specific Gene ◽  
Significant Differential Expression ◽  
Nac Transcription Factors ◽  
Functional Relationships

Abstract Background Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. Results To clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate. Conclusions This finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower.

scholarly journals Mosaic evolution of molecular pathways for sex pheromone communication in a butterfly

2020 ◽  
Author(s):  
Caroline M. Nieberding ◽  
Patrícia Beldade ◽  
Véronique Baumlé ◽  
Gilles San Martin ◽  
Alok Arun ◽  
...  
Keyword(s):  
Sex Pheromone ◽  
Large Scale ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Pheromone Biosynthesis ◽  
Specific Gene ◽  
Evolutionary Divergence ◽  
Molecular Pathways ◽  
Pheromone Communication ◽  
Bicyclus Anynana

AbstractUnraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved, ancestral traits, and newly evolved, derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~98 million years ago. In moths, females typically emit pheromones to attract male mates, but in butterflies pheromones and used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but have remained virtually unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics, to identify genes involved in different steps of sex pheromone communication in the butterfly Bicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana further appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulation of sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale analysis of the genetic pathways underlying sex pheromone communication in a butterfly.

scholarly journals Relative mutation rates of each nucleotide for another estimated from allele frequency spectra at human gene loci

2009 ◽  
Vol 91 (4) ◽  
pp. 293-303 ◽  
Author(s):  
LEEYOUNG PARK
Keyword(s):  
Large Scale ◽  
Human Gene ◽  
Basic Theory ◽  
Equilibrium Analysis ◽  
Mutation Rates ◽  
Specific Gene ◽  
Sequencing Data ◽  
Cytosine Deamination ◽  
Frequency Spectra ◽  
Estimated Parameters

SummaryThis study aims to comprehensively examine the mutation rates of one base for another in human gene loci. In contrast to most previous efforts based on divergence data from untranscribed regions, the present study employs the basic theory of the reversible recurrent mutation model using large-scale, high-quality re-sequencing data from public databases of gene loci. Population mutation parameters (4Nν and 4Nμ) are obtained for each pair of base substitutions. The estimated parameters show good strand reversal symmetry, supporting the existence of mutation-drift equilibrium. Analysis of specific gene regions including mRNA, coding sequence (CDS), 5′-untranslated region (5′-UTRs), 3′-UTR and intron shows that there are clear differences in the mutation rates of each base for another depending on the location of the base in question. Results from analyses that take the adjacent bases into account exhibit excellent strand reversal symmetry, confirming that the identity of an adjacent base influences mutation rates. The CpG to TpG (or CpG to CpA) substitution is found at a rate approximately seven-fold higher than the reverse transition in intron regions due to cytosine deamination, but the effect is strongly reduced in mRNA regions and almost entirely lost in 5′-UTRs. However, from the overall increased transitions in sites other than CpGs and the proportion of CpGs in the total sequence, CpG methylation is not the main factor responsible for the increased rate of transitions as compared with transversions. In this report, after adjusting average mutation rates to the sequence compositions, no substitution bias is found between A+T and C+G, indicating base composition equilibrium in human gene loci. Population differences are also identified between groups of people of African and European descent, presumably due to past population histories. By applying the basic theory of population genetics to re-sequenced data, this study contributes new, detailed information regarding mutations in human gene regions.

scholarly journals Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Adam Pym ◽  
Kumar Saurabh Singh ◽  
Åsa Nordgren ◽  
T. G. Emyr Davies ◽  
Christoph T. Zimmer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Host Plants ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Wide Spectrum ◽  
Transcriptome Profiling ◽  
Gene Families ◽  
Trialeurodes Vaporariorum ◽  
Specific Gene ◽  
Natural And Synthetic

Abstract Background The glasshouse whitefly, Trialeurodes vaporariorum, is a damaging crop pest and an invasive generalist capable of feeding on a broad range of host plants. As such this species has evolved mechanisms to circumvent the wide spectrum of anti-herbivore allelochemicals produced by its host range. T. vaporariorum has also demonstrated a remarkable ability to evolve resistance to many of the synthetic insecticides used for control. Results To gain insight into the molecular mechanisms that underpin the polyphagy of T. vaporariorum and its resistance to natural and synthetic xenobiotics, we sequenced and assembled a reference genome for this species. Curation of genes putatively involved in the detoxification of natural and synthetic xenobiotics revealed a marked reduction in specific gene families between this species and another generalist whitefly, Bemisia tabaci. Transcriptome profiling of T. vaporariorum upon transfer to a range of different host plants revealed profound differences in the transcriptional response to more or less challenging hosts. Large scale changes in gene expression (> 20% of genes) were observed during adaptation to challenging hosts with a range of genes involved in gene regulation, signalling, and detoxification differentially expressed. Remarkably, these changes in gene expression were associated with significant shifts in the tolerance of host-adapted T. vaporariorum lines to natural and synthetic insecticides. Conclusions Our findings provide further insights into the ability of polyphagous insects to extensively reprogram gene expression during host adaptation and illustrate the potential implications of this on their sensitivity to synthetic insecticides.

scholarly journals VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Sara Silva Pereira ◽  
John Heap ◽  
Andrew R Jones ◽  
Andrew P Jackson
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Variant Calling ◽  
Gene Families ◽  
Automated Analysis ◽  
Surface Glycoprotein ◽  
Sequencing Data ◽  
High Throughput Analysis ◽  
African Trypanosomes ◽  
Variant Antigen

Abstract Background Analysing variant antigen gene families on a population scale is a difficult challenge for conventional methods of read mapping and variant calling due to the great variability in sequence, copy number, and genomic loci. In African trypanosomes, hemoparasites of humans and animals, this is complicated by variant antigen repertoires containing hundreds of genes subject to various degrees of sequence recombination. Findings We introduce Variant Antigen Profiler (VAPPER), a tool that allows automated analysis of the variant surface glycoprotein repertoires of the most prevalent livestock African trypanosomes. VAPPER produces variant antigen profiles for any isolate of the veterinary pathogens Trypanosoma congolense and Trypanosoma vivax from genomic and transcriptomic sequencing data and delivers publication-ready figures that show how the queried isolate compares with a database of existing strains. VAPPER is implemented in Python. It can be installed to a local Galaxy instance from the ToolShed (https://toolshed.g2.bx.psu.edu/) or locally on a Linux platform via the command line (https://github.com/PGB-LIV/VAPPER). The documentation, requirements, examples, and test data are provided in the Github repository. Conclusion By establishing two different, yet comparable methodologies, our approach is the first to allow large-scale analysis of African trypanosome variant antigens, large multi-copy gene families that are otherwise refractory to high-throughput analysis.

scholarly journals Transcription shifts in gut bacteria shared between mothers and their infants: data from the NiPPeR Study

2021 ◽  
Author(s):  
Tommi Vatanen ◽  
Olga Sakwinska ◽  
Brooke Wilson ◽  
Severine Combremont ◽  
Wayne Cutfield ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Gene Families ◽  
Gut Bacteria ◽  
Sequencing Data ◽  
Bacterial Strains ◽  
Bacterial Gene ◽  
Bacterial Gene Expression ◽  
Infant Gut Microbiome ◽  
Dependent Strain

Abstract The infant gut microbiome contains a portion of bacteria that originate from the maternal gut. In the infant gut these bacteria encounter a new metabolic environment that differs from the adult gut, consequently requiring adjustments in their activities. We utilized community RNA sequencing data (metatranscriptomes) from ten mother-infant dyads participating in the NiPPeR Study to characterize bacterial gene expression shifts following mother-to-infant transmission. Maternally derived bacterial strains adapted by large scale gene expression shifts following the transmission to the infant gut, with 12,564 activated and 14,844 deactivated gene families, including 1,007 transferases and 85 bacteriophage genes. The implicated genes were most numerous and the magnitude shifts greatest in Bacteroides spp. This study demonstrates environment-dependent, strain-specific shifts in gut bacteria function and underscores the importance of metatranscriptomic analysis in microbiome studies.

scholarly journals The genome of Nautilus pompilius illuminates eye evolution and biomineralization

2021 ◽  
Author(s):  
Yang Zhang ◽  
Fan Mao ◽  
Huawei Mu ◽  
Minwei Huang ◽  
Yongbo Bao ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Gene Families ◽  
Low Complexity ◽  
Specific Gene ◽  
Valuable Resource ◽  
Nautilus Pompilius ◽  
Coding Regions ◽  
Eye Evolution ◽  
Encoding Genes ◽  
Contraction And Expansion

AbstractNautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.

scholarly journals Genome-Wide Analysis of NAC Transcription Factors in Sunflower (Helianthus Annuus), Their Comparative Phylogenetic Analysis and Association With Leaf Senescence

2021 ◽  
Author(s):  
Sofia A. Bengoa Luoni ◽  
Alberto Cenci ◽  
Sebastian Moschen ◽  
Salvador Nicosia ◽  
Laura M. Radonic ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Leaf Senescence ◽  
Large Scale ◽  
Gene Families ◽  
Orthologous Group ◽  
Specific Gene ◽  
Significant Differential Expression ◽  
Nac Transcription Factors ◽  
Functional Relationships

Abstract Background Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. ResultsTo clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate.ConclutionsThis finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower.

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