scholarly journals First report of reference guided genome assembly of Black Bengal goat (Capra hircus)

2019 ◽  
Author(s):  
Amam Z. Siddiki ◽  
A. Baten ◽  
M. Billah ◽  
MAU. Alam ◽  
KSM. Shawrob ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Capra Hircus ◽  
Sequencing Platform ◽  
Gene Annotations ◽  
Skin Quality ◽  
Genome Information ◽  
Black Bengal Goat ◽  
Illumina Sequencing Platform

AbstractObjectivesBlack Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest.Data descriptionThe genomic DNA of local (Chittagong, Bangladesh) healthy Black Bengal goat (Capra hircus) was extracted and then sequenced. The de novo assembly and structural annotations are being presented here. Sequencing was done using Illumina sequencing platform and the draft genome assembled is about 3.04 Gb. 26458 Genes were annotated using Maker gene annotations tool which predicted BUSCO Gene models. Universal Single Copy Orthologs refer 82.5% completeness of the assembled genome.

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 De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration

2020 ◽  
Vol 10 (10) ◽  
pp. 3541-3548
Author(s):  
Simon Yung Wa Sin ◽  
Lily Lu ◽  
Scott V. Edwards
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Genomic Region ◽  
Plumage Coloration ◽  
Sexual Dichromatism ◽  
Effective Population ◽  
Cardinalis Cardinalis ◽  
Northern Cardinal ◽  
Genomic Studies

Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly-contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene in C. cardinalis. Transcription factor binding motifs discovered in the unique insertion region in C. cardinalis suggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000–250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome of C. cardinalis provides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.

scholarly journals De Novo Whole-Genome Sequencing of the Wood Rot Fungus Polyporus brumalis, Which Exhibits Potential Terpenoid Metabolism

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Su-Yeon Lee ◽  
Ji-eun An ◽  
Sun-Hwa Ryu ◽  
Myungkil Kim
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Gene Annotation ◽  
Draft Genome ◽  
Fungal Growth ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Protein Coding Genes ◽  
Polyporus Brumalis ◽  
Terpenoid Metabolism

ABSTRACT Polyporus brumalis is able to synthesize several sesquiterpenes during fungal growth. Using a single-molecule real-time sequencing platform, we present the 53-Mb draft genome of P. brumalis, which contains 6,231 protein-coding genes. Gene annotation and isolation support genetic information, which can increase the understanding of sesquiterpene metabolism in P. brumalis.

scholarly journals Draft genome of the Reindeer (Rangifer tarandus)

2017 ◽  
Author(s):  
Zhipeng Li ◽  
Zeshan Lin ◽  
Lei Chen ◽  
Hengxing Ba ◽  
Yongzhi Yang ◽  
...  
Keyword(s):  
Rangifer Tarandus ◽  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Divergence Time ◽  
Capra Hircus ◽  
High Quality ◽  
Illumina Hiseq

AbstractBackgroundReindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids’ milk. A high quality reference genome of this specie will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus, and ancestors of Bos taurus and Capra hircus, is estimated to be 29.55 million years ago (Mya).ConclusionsOur results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

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 Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum)

2020 ◽  
Vol 10 (10) ◽  
pp. 3489-3495
Author(s):  
Natascha van Lieshout ◽  
Ate van der Burgt ◽  
Michiel E. de Vries ◽  
Menno ter Maat ◽  
David Eickholt ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Reference Genome ◽  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
Rapid Expansion ◽  
Potato Genome ◽  
Homozygous Diploid ◽  
Gene Orthologs ◽  
Reference Genomes

With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated “DM”, has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of Solyntus as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, Solyntus provides a more direct and contiguous reference then ever before available. It was constructed by sequencing with state-of-the-art long and short read technology and assembled with Canu. The 116 contigs were assembled into scaffolds to form each pseudochromosome, with three contigs to 17 contigs per chromosome. This assembly contains 93.7% of the single-copy gene orthologs from the Solanaceae set and has an N50 of 63.7 Mbp. The genome and related files can be found at https://www.plantbreeding.wur.nl/Solyntus/. With the release of this research line and its draft genome we anticipate many exciting developments in (diploid) potato research.

scholarly journals Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms

Pathogens ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 834
Author(s):  
Xinxin Wang ◽  
Jingyu Peng ◽  
Lei Sun ◽  
Gregory Bonito ◽  
Yuxiu Guo ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Gene Clusters ◽  
Single Copy ◽  
Dual Culture ◽  
Edible Fungi ◽  
Fungal Cell ◽  
Sequencing Platform ◽  
Phylogenetic Placement

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.

scholarly journals Whole-Genome Sequence of Salmonella enterica Serovar Enteritidis Phage Type 4, Isolated from a Brazilian Poultry Farm

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Guilherme Paier Milanez ◽  
Leandro Costa Nascimento ◽  
Adriane Holtz Tirabassi ◽  
Marcelo Zuanaze ◽  
Dália Prazeres Rodrigues ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Phage Type ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Poultry Farm ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Sequencing Platform ◽  
Paulo State ◽  
Illumina Sequencing Platform

The draft genome of Salmonella enterica serovar Enteritidis phage type 4 (PT4) strain IOC4647/2004, isolated from a poultry farm in São Paulo state, was obtained with high-throughput Illumina sequencing platform, generating 4,173,826 paired-end reads with 251 bp. The assembly of 4,804,382 bp in 27 scaffolds shows strong similarity to other S . Enteritidis strains.

scholarly journals The First Draft Genome Assembly of Snow Sheep (Ovis nivicola)

2020 ◽  
Vol 12 (8) ◽  
pp. 1330-1336 ◽  
Author(s):  
Maulik Upadhyay ◽  
Andreas Hauser ◽  
Elisabeth Kunz ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Single Copy ◽  
Climatic Conditions ◽  
Draft Genome Assembly ◽  
Sheep Genome ◽  
Long Reads

Abstract The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (∼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.

scholarly journals Cloning and Functional Analysis of Three Chalcone Synthases from the Flowers of Safflowers Carthamus tinctorius

2016 ◽  
Vol 11 (6) ◽  
pp. 1934578X1601100 ◽  
Author(s):  
Junichi Shinozaki ◽  
Hiromichi Kenmoku ◽  
Kenichi Nihei ◽  
Kazuo Masuda ◽  
Masaaki Noji ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Dna Sequences ◽  
Chalcone Synthase ◽  
De Novo ◽  
Sole Source ◽  
Carthamus Tinctorius ◽  
Sequencing Platform ◽  
Traditional Medicines ◽  
Chalcone Synthase Genes ◽  
Illumina Sequencing Platform

The flowers of safflowers (Carthamus tinctorius L.) are very important as they are the sole source of their distinct pigments, i.e. carthamus-red and-yellows, and have historically had strong connections to the cultural side of human activities such as natural dyes, rouge, and traditional medicines. The distinct pigments are quinochalcone C-glucosides, which are found specifically in the flowers of C. tinctorius. To investigate the biosynthetic pathways of quinochalcone C-glucosides, de novo assembly of the transcriptome was performed on the flowers using an Illumina sequencing platform to obtain 69,312 annotated coding DNA sequences. Three chalcone synthase like genes, CtCHSl, 2 and 3 were focused on and cloned, which might be involved in quinochalcone C-glucosides biosynthesis by establishing the C6-C3-C6 chalcone skeleton. It was demonstrated that all the recombinant CtCHSs could recognize p-coumaroyl-CoA, caffeoyl-CoA, feruloyl-CoA, and sinapoyl-CoA as starter substrates. This is the first report on the cloning and functional analysis of the three chalcone synthase genes from the flowers of C. tinctorius.

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