scholarly journals Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

2019 ◽  
Author(s):  
Haley Wight ◽  
Junhui Zhou ◽  
Muzi Li ◽  
Sridhar Hannenhalli ◽  
Stephen M. Mount ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Rubus Idaeus ◽  
Slow Process ◽  
Red Raspberry ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Protein Coding Genes ◽  
A Genome ◽  
Exceptional Value

AbstractThe red raspberry, Rubus idaeus, is widely distributed in all temperate regions of Europe, Asia, and North America and is a major commercial fruit valued for its taste, high antioxidant and vitamin content. However, Rubus breeding is a long and slow process hampered by limited genomic and molecular resources. Genomic resources such as a complete genome sequencing and transcriptome will be of exceptional value to improve research and breeding of this high value crop. Using a hybrid sequence assembly approach including data from both long and short sequence reads, we present the first assembly of the Rubus idaeus genome (Joan J. variety). The de novo assembled genome consists of 2,145 scaffolds with a genome completeness of 95.3% and an N50 score of 638 KB. Leveraging a linkage map, we anchored 80.1% of the genome onto seven chromosomes. Using over 1 billion paired-end RNAseq reads, we annotated 35,566 protein coding genes with a transcriptome completeness score of 97.2%. The Rubus idaeus genome provides an important new resource for researchers and breeders.

scholarly journals Draft Genome Assembly of Filamentous Brackish Cyanobacterium Limnoraphis robusta Strain CS-951

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Anusuya Willis ◽  
Matthew Parks ◽  
Michele A. Burford
Keyword(s):  
Genome Assembly ◽  
Brackish Water ◽  
Draft Genome ◽  
Gc Content ◽  
Lyngbya Majuscula ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Putative Protein ◽  
Protein Coding Genes ◽  
A Genome

Limnoraphis robusta CS-951 is a sheathed, filamentous benthic, nonheterocystous cyanobacterium. It was isolated from brackish water and identified morphologically as Lyngbya majuscula . We report the draft genome of L. robusta CS-951, with a genome size of 7,314,117 bp, a 41.6% GC content, and 6,791 putative protein-coding genes assembled into 361contigs.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

scholarly journals Draft Genome of the Macadamia Husk Spot Pathogen, Pseudocercospora macadamiae

2020 ◽  
Vol 110 (9) ◽  
pp. 1503-1506
Author(s):  
Olufemi A. Akinsanmi ◽  
Lilia C. Carvalhais
Keyword(s):  
Plant Disease Resistance ◽  
Plant Disease ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Disease Development ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family

Pseudocercospora macadamiae causes husk spot in macadamia in Australia. Lack of genomic resources for this pathogen has restricted acquiring knowledge on the mechanism of disease development, spread, and its role in fruit abscission. To address this gap, we sequenced the genome of P. macadamiae. The sequence was de novo assembled into a draft genome of 40 Mb, which is comparable to closely related species in the family Mycosphaerellaceae. The draft genome comprises 212 scaffolds, of which 99 scaffolds are over 50 kb. The genome has a 49% GC content and is predicted to contain 15,430 protein-coding genes. This draft genome sequence is the first for P. macadamiae and represents a valuable resource for understanding genome evolution and plant disease resistance.

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 Sequence of a Novel Bacterium,Pseudomonassp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West Bengal, India

2018 ◽  
Vol 6 (3) ◽  
pp. e01443-17 ◽  
Author(s):  
Vivek Kumar Ranjan ◽  
Tilak Saha ◽  
Shriparna Mukherjee ◽  
Ranadhir Chakraborty
Keyword(s):  
Genome Sequence ◽  
West Bengal ◽  
Draft Genome ◽  
Homogentisic Acid ◽  
Draft Genome Sequence ◽  
Gene Length ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Novel Bacterium ◽  
A Genome

ABSTRACTThe draft genome sequence of a novel strain,Pseudomonassp. MR 02, a pyomelanin-producing bacterium isolated from the Mahananda River at Siliguri, West Bengal, India, is reported here. This strain has a genome size of 5.94 Mb, with an overall G+C content of 62.6%. The draft genome reports 5,799 genes (mean gene length, 923 bp), among which 5,503 are protein-coding genes, including the genes required for the catabolism of tyrosine or phenylalanine for the characteristic production of homogentisic acid (HGA). Excess HGA, on excretion, auto-oxidizes and polymerizes to form pyomelanin.

scholarly journals A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)

2020 ◽  
Author(s):  
Qiye Li ◽  
Qunfei Guo ◽  
Yang Zhou ◽  
Huishuang Tan ◽  
Terry Bertozzi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Protein Coding ◽  
Large Genome ◽  
Draft Genome Assembly ◽  
Protein Coding Genes ◽  
Repeat Content ◽  
Australian Continent ◽  
Large Genome Size ◽  
Reference Genomes

AbstractAmphibian genomes are usually challenging to assemble due to large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.

scholarly journals A draft genome sequence of the elusive giant squid, Architeuthis dux

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Rute R da Fonseca ◽  
Alvarina Couto ◽  
Andre M Machado ◽  
Brona Brejova ◽  
Carolin B Albertin ◽  
...  
Keyword(s):  
Deep Sea ◽  
Draft Genome ◽  
Deep Ocean ◽  
High Arctic ◽  
Dosidicus Gigas ◽  
Final Size ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Giant Squid ◽  
A Genome

ABSTRACT Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

scholarly journals A high-quality chromosomal genome assembly of Diospyros oleifera Cheng

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Yujing Suo ◽  
Peng Sun ◽  
Huihui Cheng ◽  
Weijuan Han ◽  
Songfeng Diao ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Diospyros Kaki ◽  
High Quality ◽  
Phylogenetic Tree Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Anthocyanin Pathway

Abstract Background Diospyros oleifera Cheng, of the family Ebenaceae, is an economically important tree. Phylogenetic analyses indicate that D. oleifera is closely related to Diospyros kaki Thunb. and could be used as a model plant for studies of D. kaki. Therefore, development of genomic resources of D. oleifera will facilitate auxiliary assembly of the hexaploid persimmon genome and elucidate the molecular mechanisms of important traits. Findings The D. oleifera genome was assembled with 443.6 Gb of raw reads using the Pacific Bioscience Sequel and Illumina HiSeq X Ten platforms. The final draft genome was ∼812.3 Mb and had a high level of continuity with N50 of 3.36 Mb. Fifteen scaffolds corresponding to the 15 chromosomes were assembled to a final size of 721.5 Mb using 332 scaffolds, accounting for 88.81% of the genome. Repeat sequences accounted for 54.8% of the genome. By de novo sequencing and analysis of homology with other plant species, 30,530 protein-coding genes with an average transcript size of 7,105.40 bp were annotated; of these, 28,580 protein-coding genes (93.61%) had conserved functional motifs or terms. In addition, 171 candidate genes involved in tannin synthesis and deastringency in persimmon were identified; of these chalcone synthase (CHS) genes were expanded in the D. oleifera genome compared with Diospyros lotus, Camellia sinensis, and Vitis vinifera. Moreover, 186 positively selected genes were identified, including chalcone isomerase (CHI) gene, a key enzyme in the flavonoid-anthocyanin pathway. Phylogenetic tree analysis indicated that the split of D. oleifera and D. lotus likely occurred 9.0 million years ago. In addition to the ancient γ event, a second whole-genome duplication event occurred in D. oleifera and D. lotus. Conclusions We generated a high-quality chromosome-level draft genome for D. oleifera, which will facilitate assembly of the hexaploid persimmon genome and further studies of major economic traits in the genus Diospyros.

scholarly journals Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

2018 ◽  
Vol 6 (16) ◽  
pp. e00265-18 ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Edward J. Marr ◽  
Harry W. Wright ◽  
Robert J. Weaver ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Psoroptes Ovis ◽  
Protein Coding ◽  
Content Type ◽  
Sheep Scab ◽  
Draft Genome Assembly ◽  
Intense Pruritus

ABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of P. ovis based on PacBio de novo sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.

scholarly journals Draft Genome Sequence of Escherichia coli KL53

2018 ◽  
Vol 6 (13) ◽  
Author(s):  
Katarina Soltys ◽  
Silvia Vavrova ◽  
Jaroslav Budis ◽  
Lenka Palkova ◽  
Gabriel Minarik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Clinical Isolate ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Tellurite Resistance ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

ABSTRACT Here, we report the draft genome sequence of a clinical isolate of the uropathogenic strain Escherichia coli KL53. A total of 5,083,632 bp was de novo assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes. Remarkable is the presence of the tellurite resistance ( ter ) operon on a plasmid.

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