scholarly journals Fully resolved assembly of Cryptosporidium parvum

2021 ◽  
Author(s):  
Vipin K. Menon ◽  
Pablo C. Okhuysen ◽  
Cynthia Chappell ◽  
Medhat Mahmoud ◽  
Qingchang Meng ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Reference Genome ◽  
Single Copy ◽  
Comparative Genomic ◽  
Infection Prevalence ◽  
High Quality ◽  
Apicomplexan Parasites ◽  
Oxford Nanopore ◽  
Genomic Study ◽  
Genomic Studies

Background Cryptosporidium parvum are apicomplexan parasites commonly found across many species with a global infection prevalence of 7.6%. As such it is important to understand the diversity and genomic makeup of this prevalent parasite to prohibit further spread and to fight an infection. The general basis of every genomic study is a high quality reference genome that has continuity and completeness, and is of high quality and thus enables comprehensive comparative studies. Findings Here we provide a highly accurate and complete reference genome of Cryptosporidium spp.. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall the assembly shows a high completion rate with 98.4% single copy Busco genes. This is also shown by the identification of 13 telomeric regions across the 8 chromosomes. The consensus accuracy of the established reference genome was further validated by sequence alignment of established genetic markers for C.parvum. Conclusions This high quality reference genome provides the basis for subsequent studies and comparative genomic studies across the Cryptosporidium clade.

scholarly journals Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China

2021 ◽  
Author(s):  
Yuanchao Liu ◽  
Longhua Huang ◽  
Huiping Hu ◽  
Manjun Cai ◽  
Xiaowei Liang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Southwest China ◽  
Reference Genome ◽  
Biological Activities ◽  
Single Copy ◽  
The Tibetan Plateau ◽  
Whole Genome ◽  
High Quality ◽  
Pharmacological Activities ◽  
Genetic Studies

Abstract Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaffold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

2020 ◽  
Vol 33 (5) ◽  
pp. 718-720
Author(s):  
Karthi Natesan ◽  
Ji Yeon Park ◽  
Cheol-Woo Kim ◽  
Dong Suk Park ◽  
Young-Seok Kwon ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Gc Content ◽  
Comparative Genomic ◽  
High Quality ◽  
Sequencing Platform ◽  
Peronospora Destructor ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

scholarly journals Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Feng Shao ◽  
Arne Ludwig ◽  
Yang Mao ◽  
Ni Liu ◽  
Zuogang Peng
Keyword(s):  
Dna Sequences ◽  
Genome Assembly ◽  
Gambusia Affinis ◽  
Comparative Genomic ◽  
Suitable Model ◽  
High Quality ◽  
Western Mosquitofish ◽  
Poeciliid Fish ◽  
Oxford Nanopore ◽  
Chromosome Level

Abstract Background The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it. Results The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated. Conclusions The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.

scholarly journals High-quality assembly of sweet basil genome

2018 ◽  
Author(s):  
Nativ Dudai ◽  
Marie-Jeanne Carp ◽  
Renana Milavski ◽  
David Chaimovitsh ◽  
Alona Shachter ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
High Quality ◽  
Sweet Basil ◽  
Independent Analysis ◽  
Aroma Production ◽  
Culinary Uses ◽  
Underlying Mechanisms ◽  
Sequencing Platforms

AbstractSweet basil, sometimes called the King of Herbs, is well known for its culinary uses, especially in the Italian sauce ‘Pesto’. It is also used in traditional medicine, as a source for essential oils and as an ornamental plant. So far, basil was bred by classical and traditional methods due to lack of a reference genome that will allow optimized application of the most up-to-date sequencing techniques. Here, we report on the first completion of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil, using several next generation sequencing platforms followed by genome assembly with NRGENE’s DeNovoMAGIC assembly tool. We determined that the genome size of sweet basil is 2.13 Gbp and assembled it into 12,212 scaffolds. The high-quality of the assembly is reflected in that more than 90% of the assembly size is composed of only 107 scaffolds. An independent analysis of single copy orthologues genes showed a 93% completeness which reveal also that 74% of them were duplicated, indicating that the sweet basil is a tetraploid organism. A reference genome of sweet basil will enable to develop precise molecular markers for various agricultural important traits such as disease resistance and tolerance to various environmental conditions. We will gain a better understanding of the underlying mechanisms of various metabolic processes such as aroma production and pigment accumulation. Finally, it will save time and money for basil breeders and scientists and ensure higher throughput and robustness in future studies.

scholarly journals A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9114 ◽  
Author(s):  
Jiawei Wang ◽  
Weizhen Liu ◽  
Dongzi Zhu ◽  
Xiang Zhou ◽  
Po Hong ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Reference Genome ◽  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
High Quality ◽  
Eukaryotic Genes

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

scholarly journals Genome Assembly of the Dogface Butterfly Zerene cesonia

2019 ◽  
Vol 12 (1) ◽  
pp. 3580-3585 ◽  
Author(s):  
Luis Rodriguez-Caro ◽  
Jennifer Fenner ◽  
Caleb Benson ◽  
Steven M Van Belleghem ◽  
Brian A Counterman
Keyword(s):  
Genome Assembly ◽  
Developmental Plasticity ◽  
Hybrid Approach ◽  
Single Copy ◽  
Z Chromosome ◽  
High Quality ◽  
Protein Coding ◽  
Genomic Change ◽  
A Genome ◽  
Genomic Studies

Abstract Comparisons of high-quality, reference butterfly, and moth genomes have been instrumental to advancing our understanding of how hybridization, and natural selection drive genomic change during the origin of new species and novel traits. Here, we present a genome assembly of the Southern Dogface butterfly, Zerene cesonia (Pieridae) whose brilliant wing colorations have been implicated in developmental plasticity, hybridization, sexual selection, and speciation. We assembled 266,407,278 bp of the Z. cesonia genome, which accounts for 98.3% of the estimated 271 Mb genome size. Using a hybrid approach involving Chicago libraries with Hi-Rise assembly and a diploid Meraculous assembly, the final haploid genome was assembled. In the final assembly, nearly all autosomes and the Z chromosome were assembled into single scaffolds. The largest 29 scaffolds accounted for 91.4% of the genome assembly, with the remaining ∼8% distributed among another 247 scaffolds and overall N50 of 9.2 Mb. Tissue-specific RNA-seq informed annotations identified 16,442 protein-coding genes, which included 93.2% of the arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO). The Z. cesonia genome assembly had ∼9% identified as repetitive elements, with a transposable element landscape rich in helitrons. Similar to other Lepidoptera genomes, Z. cesonia showed a high conservation of chromosomal synteny. The Z. cesonia assembly provides a high-quality reference for studies of chromosomal arrangements in the Pierid family, as well as for population, phylo, and functional genomic studies of adaptation and speciation.

scholarly journals Construction of a chromosome-scale long-read reference genome assembly for potato

GigaScience ◽  
2020 ◽  
Vol 9 (9) ◽  
Author(s):  
Gina M Pham ◽  
John P Hamilton ◽  
Joshua C Wood ◽  
Joseph T Burke ◽  
Hainan Zhao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Agronomic Traits ◽  
Solanum Tuberosum L ◽  
Fold Increase ◽  
High Quality ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

Abstract Background Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1–3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost. Findings Here, we present an updated version of the DM1–3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Conclusions Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.

scholarly journals A high-quality reference genome for a parasitic bivalve with doubly uniparental inheritance (Bivalvia: Unionida)

2021 ◽  
Author(s):  
Chase H Smith
Keyword(s):  
Single Molecule ◽  
Reference Genome ◽  
Economic Value ◽  
Freshwater Mussel ◽  
Uniparental Inheritance ◽  
Doubly Uniparental Inheritance ◽  
High Quality ◽  
Long Reads ◽  
A Genome ◽  
Genomic Studies

Abstract From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.

scholarly journals A high quality reference genome for the fish pathogen Streptococcus iniae

2019 ◽  
Author(s):  
Areej S. Alsheikh-Hussain ◽  
Nouri L. Ben Zakour ◽  
Brian M. Forde ◽  
Oleksandra Silayeva ◽  
Andrew C. Barnes ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Reference Genome ◽  
South Australia ◽  
Economic Problem ◽  
Fish Mortality ◽  
Comparative Genomic ◽  
Streptococcus Iniae ◽  
High Quality ◽  
Long Range Pcr ◽  
Assembly Error

AbstractFish mortality caused by Streptococcus iniae is a major economic problem in fish aquaculture in warm and temperate regions globally. There is also risk of zoonotic infection by S. iniae through handling of contaminated fish. In this study, we present the complete genome sequence of S. iniae strain QMA0248, isolated from farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 carries a 32 Kb prophage, a 12 Kb genomic island, and 92 discrete insertion sequence (IS) elements. These include 9 novel IS types that belong mostly to the IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and publicly available complete S. iniae genomes revealed discrepancies that are likely due to misassembly in the genomes of isolates ISET0901 and ISNO. We also determined by long-range PCR that a tandem duplication of an rRNA region in the PacBio assembly of QMA0248 was an assembly error. A similar rRNA duplication in the PacBio genome of S. iniae 89353 may also be a misassembly. Our study not only highlights assembly problems in existing genomes, but provides a high quality reference genome for S. iniae QMA0248, including manually curated mobile genetic elements, that will assist future S. iniae comparative genomic and evolutionary studies.

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