scholarly journals A draft genome assembly for the eastern fox squirrel, Sciurus niger

2021 ◽  
Author(s):  
Lin Kang ◽  
Pawel Michalak ◽  
Eric Hallerman ◽  
Nancy D Moncrief
Keyword(s):  
Genome Assembly ◽  
Population Genomics ◽  
Coat Color ◽  
Genome Structure ◽  
Draft Genome ◽  
Predicted Amino Acid Sequence ◽  
Sciurus Niger ◽  
Sequence Alignments ◽  
A Genome ◽  
Fox Squirrel

Abstract The eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2.99 Gb, containing 32,830 scaffolds with an average size of 90.9 Kb and N50 of 183.8 Kb. Genome completeness was estimated to be 93.78%. A total of 24,443 protein-encoding genes were predicted from the assembly and 23,079 (94.42%) were annotated. Repeat elements comprised an estimated 38.49% of the genome, with the majority being LINEs (13.92%), SINEs (6.04%), and LTR elements. The topology of the species tree reconstructed using maximum-likelihood phylogenetic analysis was congruent with those of previous studies. This genome assembly can prove useful for comparative studies of genome structure and function in this rapidly diversifying lineage of mammals, for studies of population genomics and adaptation, and for biomedical research. Predicted amino acid sequence alignments for genes affecting heme biosynthesis, color vision, and hibernation showed point mutations and indels that may affect protein function and ecological adaptation.

scholarly journals A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 144 ◽  
Author(s):  
Laís Coelho ◽  
Lukas Musher ◽  
Joel Cracraft
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
De Novo ◽  
Structural Difference ◽  
Whole Genome ◽  
Sequencing Technology ◽  
A Genome ◽  
Avian Genomes ◽  
Chromosome Level

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

scholarly journals A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Julia Voelker ◽  
Mervyn Shepherd ◽  
Ramil Mauleon
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Genome Structure ◽  
Draft Genome ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Melaleuca Alternifolia ◽  
High Quality ◽  
Tea Tree ◽  
Prediction Approach

The economically important Melaleuca alternifolia (tea tree) is the source of a terpene-rich essential oil with therapeutic and cosmetic uses around the world. Tea tree has been cultivated and bred in Australia since the 1990s. It has been extensively studied for the genetics and biochemistry of terpene biosynthesis. Here, we report a high quality de novo genome assembly using Pacific Biosciences and Illumina sequencing. The genome was assembled into 3128 scaffolds with a total length of 362 Mb (N50  = 1.9 Mb), with significantly higher contiguity than a previous assembly (N50  = 8.7 Kb). Using a homology-based, RNA-seq evidence-based and ab initio prediction approach, 37,226 protein-coding genes were predicted. Genome assembly and annotation exhibited high completeness scores of 98.1% and 89.4%, respectively. Sequence contiguity was sufficient to reveal extensive gene order conservation and chromosomal rearrangements in alignments with Eucalyptus grandis and Corymbia citriodora genomes. This new genome advances currently available resources to investigate the genome structure and gene family evolution of M. alternifolia. It will enable further comparative genomic studies in Myrtaceae to elucidate the genetic foundations of economically valuable traits in this crop.

scholarly journals Draft Genome Sequence of Xanthobacter tagetidis ATCC 700314T

2019 ◽  
Vol 8 (28) ◽  
Author(s):  
Syeda A. Fatima ◽  
Abigail E. Goen ◽  
Kyle S. MacLea
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Gram Negative ◽  
Content Type ◽  
Degrading Bacterium ◽  
A Genome ◽  
Autotrophic Bacterium

Xanthobacter tagetidis is a thiophene-degrading bacterium associated with root balls of the plant genus Tagetes, which includes marigolds. It is a Gram-negative facultatively autotrophic bacterium with pleomorphic morphology exhibiting bent and branching rods. From strain TagT2CT (= ATCC 700314T), we report a genome assembly of 4,945,221 bp and a 69.5% G+C content.

scholarly journals Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias

Marine Drugs ◽  
2019 ◽  
Vol 17 (7) ◽  
pp. 386 ◽  
Author(s):  
Chao Bian ◽  
Jia Li ◽  
Xueqiang Lin ◽  
Xiyang Chen ◽  
Yunhai Yi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Genetic Resource ◽  
Draft Genome ◽  
Close Relative ◽  
Protein Coding ◽  
Oreochromis Aureus ◽  
Genome Wide ◽  
A Genome ◽  
Blue Tilapia ◽  
First Time

Blue tilapia (Oreochromis aureus) has been an economically important fish in Asian countries. It can grow and reproduce in both freshwater and brackish water conditions, whereas it is also considered as a significant invasive species around the world. This species has been widely used as the hybridization parent(s) for tilapia breeding with a major aim to produce novel strains. However, available genomic resources are still limited for this important tilapia species. Here, we for the first time sequenced and assembled a draft genome for a seawater cultured blue tilapia (0.92 Gb), with 97.8% completeness and a scaffold N50 of 1.1 Mb, which suggests a relatively high quality of this genome assembly. We also predicted 23,117 protein-coding genes in the blue tilapia genome. Comparisons of predicted antimicrobial peptides between the blue tilapia and its close relative Nile tilapia proved that these immunological genes are highly similar with a genome-wide scattering distribution. As a valuable genetic resource, our blue tilapia genome assembly will benefit for biomedical researches and practical molecular breeding for high resistance to various diseases, which have been a critical problem in the aquaculture of tilapias.

scholarly journals The polyploid genome of the mitotic parthenogenetic root-knot nematodeMeloidogyne enterolobii

2019 ◽  
Author(s):  
Georgios D. Koutsovoulos ◽  
Marine Poullet ◽  
Abdelnaser El Ashry ◽  
Djampa K. Kozlowski ◽  
Erika Sallet ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Resistance Genes ◽  
Genome Assembly ◽  
Genome Structure ◽  
Economic Loss ◽  
The Other ◽  
Hybrid Origin ◽  
High Coverage ◽  
Agricultural Industry ◽  
A Genome

AbstractRoot-knot nematodes (genusMeloidogyne) are plant parasitic species that cause huge economic loss in the agricultural industry and affect the prosperity of communities in developing countries. Control methods against these plant pests are sparse and the current preferred method is deployment of plant cultivars bearing resistance genes againstMeloidogynespecies. However, some species such asM. enterolobiiare not controlled by the resistance genes deployed in the most important crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Like the other most damaging Meloidogyne species (e.g.M. incognita,M. arenariaandM. javanica),M. enterolobiireproduces by obligatory mitotic parthenogenesis. Genomic singularities such as a duplicated genome structure and a relatively high proportion of transposable elements have previously been described in the above mentioned mitotic parthenogenetic Meloidogyne.To gain a better understanding of the genomic and evolutionary background we sequenced the genome ofM. enterolobiiusing high coverage short and long read technologies. The information contained in the long reads helped produce a highly contiguous genome assembly ofM. enterolobii, thus enabling us to perform high quality annotations of coding and non-coding genes, and transposable elements.The genome assembly and annotation reveals a genome structure similar to the ones described in the other mitotic parthenogenetic Meloidogyne, described as recent hybrids. Most of the genome is present in 3 different copies that show high divergence. Because most of the genes belong to these duplicated regions only few gene losses took place, which suggest a recent polyploidization. The most likely hypothesis to reconcile high divergence between genome copies despite few gene losses and translocations is also a recent hybrid origin. Consistent with this hypothesis, we found an abundance of transposable elements at least as high as the one observed in the mitotic parthenogenetic nematodesM. incognitaandM. javanica.

scholarly journals PACVr: Plastome Assembly Coverage Visualization in R

2019 ◽  
Author(s):  
Michael Gruenstaeudl ◽  
Nils Jenke
Keyword(s):  
Genome Assembly ◽  
Inverted Repeat ◽  
Plastid Genome ◽  
Genome Structure ◽  
Software Tools ◽  
Coverage Depth ◽  
Assembly Quality ◽  
Gene Synteny ◽  
Plastid Genomes ◽  
A Genome

ABSTRACTBackgroundThe circular, quadripartite structure of plastid genomes which includes two inverted repeat regions renders the automatic assembly of plastid genomes challenging. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on plastid genome structure and evolution. Plastome-based phylogenetic or population genetic investigations, for example, require the precise identification of DNA sequence and length to determine the location of nucleotide polymorphisms. The average coverage depth of a genome assembly is often used as an indicator for assembly quality. Visualizing coverage depth across a draft genome allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Based on such visualizations, users can conduct a local re-assembly or other forms of targeted error correction. Few, if any, contemporary software tools can visualize the coverage depth of a plastid genome assembly while taking its quadripartite structure into account, despite the interplay between genome structure and assembly quality. A software tool is needed that visualizes the coverage depth of a plastid genome assembly on a circular, quadripartite map of the plastid genome.ResultsWe introduce ‘PACVr’, an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as to the individual plastome genes. The tool allows visualizations on different scales using a variable window approach and also visualizes the equality of gene synteny in the inverted repeat regions of the plastid genome, thus providing an additional measure of assembly quality. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be directly invoked from a Unix shell, thus facilitating its use in automated quality control. We illustrate the application of PACVr on two empirical datasets and compare the resulting visualizations with alternative software tools for displaying plastome sequencing coverage.ConclusionsPACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) the equality of gene synteny in the inverted repeat regions. It, thus, contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences, especially in light of incongruence among the visualization results of alternative software tools. The software, example datasets, technical documentation, and a tutorial are available with the package at https://github.com/michaelgruenstaeudl/PACVr.

scholarly journals Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution

2015 ◽  
Author(s):  
John Davey ◽  
Mathieu Chouteau ◽  
Sarah L. Barker ◽  
Luana Maroja ◽  
Simon W. Baxter ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Chromosome Fusion ◽  
Short Read Sequencing ◽  
A Genome ◽  
Heliconius Melpomene ◽  
Long Read ◽  
In The Wild ◽  
Chromosome Fusions ◽  
Genome Assemblies

The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridise in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. Firstly, we whole genome sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Secondly, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Thirdly, we incorporated ~20x coverage of Pacific Biosciences sequencing and scaffolded the haploid genome using an assembly of this long read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an L50 of 2.1 Mb, an N50 of 34 and with 99% of the genome placed and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million years.

scholarly journals De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)

2021 ◽  
Author(s):  
Luis J Chueca ◽  
Tilman Schell ◽  
Markus Pfenninger
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Land Snail ◽  
Land Snails ◽  
Agricultural Pests ◽  
De Novo Genome Assembly ◽  
Draft Genome Assembly ◽  
Western Palearctic ◽  
A Genome

Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.

scholarly journals Are personalities genetically determined? Inferences from subsocial spiders

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jessica Purcell ◽  
Jonathan N. Pruitt
Keyword(s):  
Genome Assembly ◽  
Interspecific Interactions ◽  
Draft Genome ◽  
Animal Personality ◽  
Genomic Research ◽  
Future Research ◽  
Nucleotide Polymorphisms ◽  
Behavioral Strategies ◽  
Draft Genome Assembly ◽  
A Genome

Abstract Background Recent research has revealed that polymorphic behavioral strategies shape intra-and interspecific interactions and contribute to fitness in many animal species. A better understanding of the proximate mechanisms underlying these behavioral syndromes will enhance our grasp this phenomenon. Spiders in the genus Anelosimus exhibit inter-individual behavioral variation on several axes: individuals have consistent responses to stimuli (e.g. bold vs. shy individuals) and they are subsocial (exhibiting extended maternal care and sibling cooperation) across most of their range, but they sometimes form permanent social groups in northern temperate regions. Here, we seek genetic variants associated with boldness and with social structure in a socially polymorphic population of the spider Anelosimus studiosus. We also develop preliminary genomic resources, including a genome assembly and linkage map, that support this and future genomic research on this group. Results Remarkably, we identify a small genomic scaffold (~ 1200 bp) that harbors seven single nucleotide polymorphisms (SNPs) associated with boldness. Moreover, heterozygotes are less common than expected based on Hardy-Weinberg equilibrium, suggesting that either assortative mating or selection against heterozygotes may be occurring in this system. We find no loci significantly associated with social organization. Our draft genome assembly allows us to localize SNPs of interest in this study and to carry out genetic comparisons with other published genomes, although it remains highly fragmented. Conclusions By identifying a locus associated with a well-studied animal personality trait, this study opens up avenues for future research to link behavioral studies of animal personality with genotype and fitness.

scholarly journals A Genome Sequence Resource for the Geographically Widespread Anthracnose Pathogen Colletotrichum asianum

Plant Disease ◽  
2020 ◽  
Vol 104 (8) ◽  
pp. 2044-2047 ◽  
Author(s):  
Yanan Meng ◽  
Yihua Ren ◽  
Wenjing Wang ◽  
Mark L. Gleason ◽  
Rong Zhang ◽  
...  
Keyword(s):  
Species Diversity ◽  
Genetic Analysis ◽  
Genome Assembly ◽  
Plant Pathogen ◽  
Fungal Pathogens ◽  
Draft Genome ◽  
Coffee Berry ◽  
Evolutionary Mechanisms ◽  
Draft Genome Assembly ◽  
A Genome

Colletotrichum asianum is a worldwide plant pathogen causing serious fruit or leaf anthracnose diseases on a variety of plant hosts such as mango, coffee berry, chili, and other potential hosts, and it is distributed widely in Asia, America, Africa, and Oceania. This is the first genome resource available for C. asianum. The draft genome assembly will allow further analysis of species diversity and evolutionary mechanisms, and may serve as a foundation for genetic analysis that leads to greater understanding of interactions between plants and fungal pathogens.

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