scholarly journals Comparative Genomic Insights into the Longhorned Tick, Haemaphysalis Longicornis

2020 ◽  
Author(s):  
Rui-Ling Zhang ◽  
Qian Zhang ◽  
Zhong Zhang
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Animal Health ◽  
Gene Families ◽  
High Ratio ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Haemaphysalis Longicornis ◽  
Gene Set ◽  
Terrestrial Vertebrates

Abstract Background: The longhorned tick, Haemaphysalis longicornis Neumann, is widely distributed across temperate regions. It can parasitize terrestrial vertebrates, including birds and a large number of mammals. They are a concern in human and animal health notably for their potential to transmit infectious agents. Methods: Genome survey was investigated using GenomeScope v1.0.0 with a maximum k-mer coverage cutoff of 1,000. Non-redundant assembly was polished with Illumina short reads using two rounds of NextPolish v1.1.0. Genome completeness was assessed using BUSCO v3.0.2 pipeline analyses against arthropod gene set (n = 1, 066). Ab initio predictions were generated using BRAKER v2.1.5. Transcriptomic reads were mapped to the genome with HISAT2 v2.2.0 and assembled with StringTie v2.1.2. Gene functions were assigned against UniProtKB database using Diamond v0.9.24. Orthogroups of 16 Chelicerata species were inferred using OrthoFinder v2.3.8 and gene family evolution was estimated using CAFÉ v4.2.1. Gene families related to digestion and detoxification, i.e. cytochrome P450 (CYP), carboxyl/cholinesterase (CCE), glutathione-S-transferase (GST), ATP-binding cassette (ABC) transporter were annotated by searching in the genome assembly. Results: The final genome assembly has a size of 3.12 Gb, a scaffold N50 of 1.09 Mb, and captured 92.4% of the BUSCO gene set (n=1,066). Genome architecture pattern of the longhorned tick resembles another tick, Ixodes scapularis (Say), particularly in large size, highly repetitive DNA (~65%) and protein-coding genes (21,550). We also identified 5,601 non-coding RNAs with a high ratio of tRNAs (4,271). Gene family evolution revealed 350 rapidly evolving gene families. Combining function enrichment analyses of gene ontology (GO) and KEGG pathway, 255 families experiencing significant expansions mainly involves in cuticle synthesis, digestion and detoxification. Conclusions: The new genome assembly, annotation and comparative genomic analyses provide a valuable resource for insights into parasitic life mode of the longhorned tick.

scholarly journals A two-type branching process model of gene family evolution

2021 ◽  
Author(s):  
Arthur Zwaenepoel ◽  
Yves Van de Peer
Keyword(s):  
Gene Family ◽  
Process Model ◽  
Branching Process ◽  
Gene Loss ◽  
Simulated Data ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Model Parameters ◽  
Data Sets

AbstractPhylogenetic models of gene family evolution based on birth-death processes (BDPs) vide an awkward fit to comparative genomic data sets. A central assumption of these models is the constant per-gene loss rate in any particular family. Because of the possibility of partial functional redundancy among gene family members, gene loss dynamics are however likely to be dependent on the number of genes in a family, and different variations of commonly employed BDP models indeed suggest this is the case. We propose a simple two-type branching process model to better approximate the stochastic evolution of gene families by gene duplication and loss and perform Bayesian statistical inference of model parameters in a phylogenetic context. We evaluate the statistical methods using simulated data sets and apply the model to gene family data for Drosophila, yeasts and primates, providing new quantitative insights in the long-term maintenance of duplicated genes.

scholarly journals Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly

2019 ◽  
Vol 36 (10) ◽  
pp. 2143-2156 ◽  
Author(s):  
Yiyuan Li ◽  
Hyunjin Park ◽  
Thomas E Smith ◽  
Nancy A Moran
Keyword(s):  
Gene Family ◽  
Long Range ◽  
X Chromosome ◽  
Genome Assembly ◽  
Acyrthosiphon Pisum ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Pea Aphid ◽  
Structural Variations ◽  
Assembly Accuracy

Abstract Genome structural variations, including duplications, deletions, insertions, and inversions, are central in the evolution of eukaryotic genomes. However, structural variations present challenges for high-quality genome assembly, hampering efforts to understand the evolution of gene families and genome architecture. An example is the genome of the pea aphid (Acyrthosiphon pisum) for which the current assembly is composed of thousands of short scaffolds, many of which are known to be misassembled. Here, we present an improved version of the A. pisum genome based on the use of two long-range proximity ligation methods. The new assembly contains four long scaffolds (40–170 Mb), corresponding to the three autosomes and the X chromosome of A. pisum, and encompassing 86% of the new assembly. Assembly accuracy is supported by several quality assessments. Using this assembly, we identify the chromosomal locations and relative ages of duplication events, and the locations of horizontally acquired genes. The improved assembly illuminates the mode of gene family evolution by providing proximity information between paralogs. By estimating nucleotide polymorphism and coverage depth from resequencing data, we determined that many short scaffolds not assembling to chromosomes represent hemizygous regions, which are especially frequent on the highly repetitive X chromosome. Aligning the X-linked aphicarus region, responsible for male wing dimorphism, to the new assembly revealed a 50-kb deletion that cosegregates with the winged male phenotype in some clones. These results show that long-range scaffolding methods can substantially improve assemblies of repetitive genomes and facilitate study of gene family evolution and structural variation.

scholarly journals Draft genome of the Brazilian railroad worm Phrixothrix hirtus E.Olivier (Phengodidae: Coleoptera)

2021 ◽  
Author(s):  
Danilo Trabuco Amaral ◽  
Yasuo Mitani ◽  
Isabel Aparecida Silva Bonatelli ◽  
Ricardo Cerri ◽  
Yoshihiro Ohmiya ◽  
...  
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Red Light ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Families ◽  
Neotropical Region ◽  
Comparative Genomic ◽  
List Type ◽  
Draft Genome Assembly

AbstractThe Neotropical region is the richest in bioluminescent Coleoptera species, however, its bioluminescence megadiversity is still underexplored in terms of genomic organization and evolution, mainly within the Phengodidae family. The railroad worm Phrixothrix hirtus is an important biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed the partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing an important source of genomic information and a framework for comparative genomic analyses for the evaluation of the bioluminescent system in Elateroidea. The estimated genome size has ∼3.4Gb, 32% of GC content, and 67% of repetitive elements, being the largest genome described in the Elateroidea superfamily. Several events of gene family expansions associated with anatomical development and morphogenesis, as well as distinct odorant-binding receptors and retrotransposable elements were found in this genome. Similar molecular functions and biological processes are shared with other studied species of Elateriformia. Common genes putatively associated with bioluminescence production and control, including two luciferase genes that displayed 7 exons and 6 introns, and genes that could be involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea. In P. hirtus the conversion of L- to D-luciferin seems to involve additional steps using a Palmitoyl-CoA thioesterase instead of an Acyl-CoA synthetase, which was found in Lampyridae species.HighlightsFirst draft genome assembly of Phengodidae, the largest one described in Coleoptera;Gene family expansions associated with anatomical development and morphogenesis;Bioluminescent control and luciferin biosynthesis genes are common within Elateroidea;Despite similar bioluminescent system, metabolic routes may have evolved independently;

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

scholarly journals Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei

2021 ◽  
Author(s):  
Kim Vertacnik ◽  
Danielle Herrig ◽  
R Keating Godfrey ◽  
Tom Hill ◽  
Scott Geib ◽  
...  
Keyword(s):  
Gene Family ◽  
Family Size ◽  
Draft Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Gene Gain ◽  
Ecological Specialization ◽  
Dietary Specialization ◽  
Pine Sawfly ◽  
Neodiprion Lecontei

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions and characterized their genomic distributions and evolutionary history. Our results suggest that expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), and antimicrobial peptide (AMP) subfamilies may have contributed to pine adaptation. By contrast, there was no evidence of recent gene family contraction via pseudogenization. Next, we compared the number of genes in these same families across insect taxa that vary in diet, dietary specialization, and social behavior. In Hymenoptera, herbivory was associated with large GR and small olfactory receptor (OR) families, eusociality was associated with large OR and small AMP families, and--unlike investigations among more closely related taxa--ecological specialization was not related to gene family size. Overall, our results suggest that gene families that mediate ecological interactions may expand and contract predictably in response to particular selection pressures, however, the ecological drivers and temporal pace of gene gain and loss likely varies considerably across gene families.

scholarly journals Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Pingping Liang ◽  
Hafiz Sohaib Ahmed Saqib ◽  
Xiaomin Ni ◽  
Yingjia Shen
Keyword(s):  
Dna Repair ◽  
Positive Selection ◽  
Single Molecule ◽  
Genome Assembly ◽  
De Novo ◽  
Gene Families ◽  
Comparative Genomic ◽  
De Novo Genome Assembly ◽  
Marine Medaka ◽  
Oryzias Melastigma

Abstract Background Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. Results In this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses. Conclusions The highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.

scholarly journals Molecular mechanisms behind global distribution of earthworm revealed by the genome

2019 ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequences ◽  
Long Read ◽  
The Many ◽  
Related Proteins

AbstractEarthworms (Annelida: Crassiclitellata), are widely distributed around the world due to their great adaptability. However, lack of a high-quality genome sequence prevents gaining the many insights into physiology, phylogeny, and genome evolution that could come from a good earthworm genome. Herein, we report a complete genome assembly of the earthworm Amynthas corticis of about 1.2 Gb, based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the earthworm genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows 97 immune related proteins and 16S rDNA sequences shows 88 microbes with significantly response to pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, may explain its powerful defensive functions adapt to complex environment and invasion from molecular level.

scholarly journals Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes

2017 ◽  
Author(s):  
Daniel S. Carvalho ◽  
James C. Schnable ◽  
Ana Maria R. Almeida
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Gene Tree ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Phylogenetic Methods ◽  
Combined Use ◽  
Approaches To Study ◽  
Additional Support ◽  
Network Approaches

AbstractThe study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations of branches with low support in a conventional gene tree. The network approach used here may also better reflect known and suspected patterns of functional divergence relative to phylogenetic methods. Overall, we believe that the combined use of phylogenetic and network tools provide more robust assessments of gene family evolution.

scholarly journals The whale shark genome reveals patterns of vertebrate gene family evolution

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Milton Tan ◽  
Anthony K Redmond ◽  
Helen Dooley ◽  
Ryo Nozu ◽  
Keiichi Sato ◽  
...  
Keyword(s):  
Gene Family ◽  
Human Cancer ◽  
Gene Families ◽  
Immune Defense ◽  
Gene Family Evolution ◽  
Whale Shark ◽  
Ancestral Gene ◽  
Long Read ◽  
Pathogen Recognition Receptors ◽  
Major Increase

Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new Toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.

scholarly journals LARGE-SCALE GENOME SAMPLING REVEALS UNIQUE IMMUNITY AND METABOLIC ADAPTATIONS IN BATS

2021 ◽  
Author(s):  
Diana Moreno Santillan ◽  
Tanya Lama ◽  
Yocelyn Gutiérrez Guerrero ◽  
Alexis Brown ◽  
Paul Donat ◽  
...  
Keyword(s):  
Immune System ◽  
Gene Family ◽  
Molecular Mechanisms ◽  
Small Body ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Metabolic Genes ◽  
Pathway Gene ◽  
Genomic Study ◽  
Molecular Patterns

Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

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