scholarly journals Comparative analysis of corrected tiger genome provides clues to its neuronal evolution

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Parul Mittal ◽  
Shubham K. Jaiswal ◽  
Nagarjun Vijay ◽  
Rituja Saxena ◽  
Vineet K. Sharma
Keyword(s):  
Neuronal Development ◽  
Mammalian Species ◽  
Draft Genome ◽  
Evolutionary Analysis ◽  
Coding Region ◽  
Genetic Changes ◽  
Gene Sets ◽  
Development Processes ◽  
Neuronal Functions ◽  
Genome Assemblies

AbstractThe availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.

scholarly journals Comparative analysis of corrected tiger genome provides clues to their neuronal evolution

2019 ◽  
Author(s):  
Parul Mittal ◽  
Shubham Jaiswal ◽  
Nagarjun Vijay ◽  
Rituja Saxena ◽  
Vineet K. Sharma
Keyword(s):  
Neuronal Development ◽  
Mammalian Species ◽  
Draft Genome ◽  
Evolutionary Analysis ◽  
Coding Region ◽  
Genetic Changes ◽  
Gene Sets ◽  
Development Processes ◽  
Neuronal Functions ◽  
Genome Assemblies

AbstractThe availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are very sensitive to errors in genome sequences and thus require accurate genomic assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger, which was also validated by resequencing of a Bengal tiger genome and transcriptome. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard, and using five different methods at three hierarchical levels i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing the signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to be significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behavior in tiger.

scholarly journals Sex-specific regulation of neuronal functions in Caenorhabditis elegans: the sex-determining protein TRA-1 represses goa-1/Gα(i/o)

2019 ◽  
Vol 295 (2) ◽  
pp. 357-371 ◽  
Author(s):  
Vera Kutnyánszky ◽  
Balázs Hargitai ◽  
Bernadette Hotzi ◽  
Mónika Kosztelnik ◽  
Csaba Ortutay ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
Fundamental Problem ◽  
Male Mating ◽  
Coding Region ◽  
X Chromosomes ◽  
Sensory Stimuli ◽  
Specific Regulation ◽  
Neuronal Functions

AbstractFemales and males differ substantially in various neuronal functions in divergent, sexually dimorphic animal species, including humans. Despite its developmental, physiological and medical significance, understanding the molecular mechanisms by which sex-specific differences in the anatomy and operation of the nervous system are established remains a fundamental problem in biology. Here, we show that in Caenorhabditis elegans (nematodes), the global sex-determining factor TRA-1 regulates food leaving (mate searching), male mating and adaptation to odorants in a sex-specific manner by repressing the expression of goa-1 gene, which encodes the Gα(i/o) subunit of heterotrimeric G (guanine–nucleotide binding) proteins triggering physiological responses elicited by diverse neurotransmitters and sensory stimuli. Mutations in tra-1 and goa-1 decouple behavioural patterns from the number of X chromosomes. TRA-1 binds to a conserved binding site located in the goa-1 coding region, and downregulates goa-1 expression in hermaphrodites, particularly during embryogenesis when neuronal development largely occurs. These data suggest that the sex-determination machinery is an important modulator of heterotrimeric G protein-mediated signalling and thereby various neuronal functions in this organism and perhaps in other animal phyla.

scholarly journals Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1336
Author(s):  
Azamat Totikov ◽  
Andrey Tomarovsky ◽  
Dmitry Prokopov ◽  
Aliya Yakupova ◽  
Tatiana Bulyonkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Biology ◽  
Threatened Species ◽  
Mammalian Species ◽  
Draft Genome ◽  
Chromosome Length ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
Genome Assemblies ◽  
Chromosome Level

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

scholarly journals Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis

2019 ◽  
Author(s):  
Thomas Hackl ◽  
Roman Martin ◽  
Karina Barenhoff ◽  
Sarah Duponchel ◽  
Dominik Heider ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Illumina Miseq ◽  
Evolutionary Analysis ◽  
High Quality ◽  
Protein Coding ◽  
Repeat Content ◽  
Genome Assemblies ◽  
Cafeteria Roenbergensis

AbstractThe heterotrophic stramenopile Cafeteria roenbergensis is a globally distributed marine bacterivorous protist. This unicellular flagellate is host to the giant DNA virus CroV and the virophage mavirus. We sequenced the genomes of four cultured C. roenbergensis strains and generated 23.53 Gb of Illumina MiSeq data (99-282 × coverage per strain) and 5.09 Gb of PacBio RSII data (13-54 × coverage). Using the Canu assembler and customized curation procedures, we obtained high-quality draft genome assemblies with a total length of 34-36 Mbp per strain and contig N50 lengths of 148 kbp to 464 kbp. The C. roenbergensis genome has a GC content of ~70%, a repeat content of ~28%, and is predicted to contain approximately 7857-8483 protein-coding genes based on a combination of de novo, homology-based and transcriptome-supported annotation. These first high-quality genome assemblies of a Bicosoecid fill an important gap in sequenced Stramenopile representatives and enable a more detailed evolutionary analysis of heterotrophic protists.

scholarly journals Bacterial genome reduction as a result of short read sequence assembly

2016 ◽  
Author(s):  
Charles H.D. Williamson ◽  
Andrew Sanchez ◽  
Adam Vazquez ◽  
Joshua Gutman ◽  
Jason W. Sahl
Keyword(s):  
Genome Assembly ◽  
Bacterial Genome ◽  
Draft Genome ◽  
Coding Region ◽  
Entire Genome ◽  
Short Read ◽  
Short Reads ◽  
Repeat Structure ◽  
Short Read Sequence ◽  
Genome Assemblies

AbstractHigh-throughput comparative genomics has changed our view of bacterial evolution and relatedness. Many genomic comparisons, especially those regarding the accessory genome that is variably conserved across strains in a species, are performed using assembled genomes. For completed genomes, an assumption is made that the entire genome was incorporated into the genome assembly, while for draft assemblies, often constructed from short sequence reads, an assumption is made that genome assembly is an approximation of the entire genome. To understand the potential effects of short read assemblies on the estimation of the complete genome, we downloaded all completed bacterial genomes from GenBank, simulated short reads, assembled the simulated short reads and compared the resulting assembly to the completed assembly. Although most simulated assemblies demonstrated little reduction, others were reduced by as much as 25%, which was correlated with the repeat structure of the genome. A comparative analysis of lost coding region sequences demonstrated that up to 48 CDSs or up to ~112,000 bases of coding region sequence, were missing from some draft assemblies compared to their finished counterparts. Although this effect was observed to some extent in 32% of genomes, only minimal effects were observed on pan-genome statistics when using simulated draft genome assemblies. The benefits and limitations of using draft genome assemblies should be fully realized before interpreting data from assembly-based comparative analyses.

scholarly journals The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

2016 ◽  
Author(s):  
John C. Schwartz ◽  
Mark S. Gibson ◽  
Dorothea Heimeier ◽  
Sergey Koren ◽  
Adam M. Phillippy ◽  
...  
Keyword(s):  
Natural Killer ◽  
Nk Cell ◽  
Balancing Selection ◽  
Mammalian Species ◽  
Draft Genome ◽  
Allelic Polymorphism ◽  
High Quality ◽  
Lectin Receptors ◽  
Differential Outcomes ◽  
Genome Assemblies

ABSTRACTNatural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-type lectin receptors encoded within the NK gene complex (NKC). Little is known about the gene content of the NKC beyond rodent and primate lineages, other than it appears to be extremely variable between mammalian groups. We compared the NKC structure between mammalian species using new high quality draft genome assemblies for cattle and goat, re-annotated sheep, pig and horse genome assemblies and the published human, rat and mouse lemur NKC. The major NKC genes are largely in syntenic positions in all eight species, with significant independent expansions and deletions between species, allowing us to present a model for NKC evolution during mammalian radiation. The ruminant species, cattle and goats, have independently evolved a second KLRC locus flanked by KLRA and KLRJ and a novel KLRH-like gene has acquired an activating tail. This novel gene has duplicated several times within cattle, while other activating receptor genes have been selectively disrupted. Targeted genome enrichment in cattle identified varying levels of allelic polymorphism between these NKC genes concentrated in the predicted extracellular ligand binding domains. This novel recombination and allelic polymorphism is consistent with NKC evolution under balancing selection, suggesting this diversity influences individual immune responses and may impact on differential outcomes of pathogen infection and vaccination.

scholarly journals Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Vikas D. Trivedi ◽  
Pramod Kumar Jangir ◽  
Rakesh Sharma ◽  
Prashant S. Phale
Keyword(s):  
Draft Genome ◽  
Degradation Pathway ◽  
Evolutionary Analysis ◽  
Extradiol Dioxygenase ◽  
Transfer Event ◽  
New Family ◽  
New Genes ◽  
Catabolic Genes ◽  
Soil Isolate ◽  
Genes Encoding

Abstract Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, ‘upper’, ‘middle’ and ‘lower’. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The ‘upper’ pathway genes were present as a part of a integron while the ‘middle’ and ‘lower’ pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.

scholarly journals In silico analyses of CD14 molecule reveals significant evolutionary diversity potentially associated with speciation and variable immune response in mammals

2019 ◽  
Author(s):  
Olanrewaju B Morenikeji ◽  
Bolaji N Thomas
Keyword(s):  
Immune Response ◽  
Complex Disease ◽  
Mammalian Species ◽  
Coding Region ◽  
Protein Protein Interaction ◽  
Species Response ◽  
Gene Coding ◽  
Protein Interactome ◽  
Mutational Hotspots ◽  
Leucine Rich Repeats

Cluster differentiation gene (CD14) is a family of monocyte differentiating genes that works in conjunction with lipopolysaccharide binding protein (LBP), forming a complex with TLR4 or LY96 to mediate innate immune response to pathogens. In this paper, we used different computational methods to elucidate the evolution of CD14 gene coding region in 14 mammalian species. Our analyses identified leucine rich repeats (LRRs) as the only significant domain across the CD14 protein of the 14 species, presenting with frequencies ranging from 1-4. Importantly, we found signal peptides located at mutational hotspots demonstrating this gene is conserved across these species. Out of the 10 selected variants analyzed in this study, only 6 were predicted to possess significant deleterious effect. Our predicted protein interactome showed a significant varying protein-protein interaction with CD14 protein across the species. This may be important for drug target and therapeutic manipulation for the treatment of many diseases. We conclude that these results contribute to our understanding of the CD14 molecular evolution, which underlays varying species response to complex disease traits.

scholarly journals De Novo Genome Assembly of the Meadow Brown Butterfly, Maniola jurtina

2020 ◽  
Vol 10 (5) ◽  
pp. 1477-1484
Author(s):  
Kumar Saurabh Singh ◽  
David J. Hosken ◽  
Nina Wedell ◽  
Richard ffrench-Constant ◽  
Chris Bass ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
De Novo Genome Assembly ◽  
Modern Biology ◽  
Final Assembly ◽  
Gene Sets ◽  
Gene Count ◽  
In The Wild ◽  
Maniola Jurtina

Meadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology. To meet this aim, a clear description of genotype is required. Here we present the draft genome sequence of M. jurtina to serve as a founding genetic resource for this species. Seven libraries were constructed using pooled DNA from five wild caught spotted females and sequenced using Illumina, PacBio RSII and MinION technology. A novel hybrid assembly approach was employed to generate a final assembly with an N50 of 214 kb (longest scaffold 2.9 Mb). The sequence assembly described here predicts a gene count of 36,294 and includes variants and gene duplicates from five genotypes. Core BUSCO (Benchmarking Universal Single-Copy Orthologs) gene sets of Arthropoda and Insecta recovered 90.5% and 88.7% complete and single-copy genes respectively. Comparisons with 17 other Lepidopteran species placed 86.5% of the assembled genes in orthogroups. Our results provide the first high-quality draft genome and annotation of the butterfly M. jurtina.

scholarly journals A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Model Organism ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Extracellular Proteome ◽  
Protein Encoding ◽  
Gene Models ◽  
Genome Assemblies ◽  
Encoding Genes

Abstract Background Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. Conclusions This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.

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