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

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.

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Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

10.1101/546135 ◽

2019 ◽

Cited By ~ 4

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.

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

10.1101/2020.03.03.971721 ◽

2020 ◽

Cited By ~ 1

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.

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First draft genome assembly and identification of SNPs from hilsa shad (Tenualosa ilisha) of the Bay of Bengal

F1000Research ◽

10.12688/f1000research.18325.1 ◽

2019 ◽

Vol 8 ◽

pp. 320 ◽

Cited By ~ 2

Author(s):

Md. Bazlur Rahman Mollah ◽

Mohd Golam Quader Khan ◽

Md Shahidul Islam ◽

Md Samsul Alam

Keyword(s):

Genome Assembly ◽

Bay Of Bengal ◽

Draft Genome ◽

Gc Content ◽

Population Connectivity ◽

Whole Genome ◽

Migratory Fish ◽

Protein Coding ◽

Protein Coding Genes ◽

Tenualosa Ilisha

Background: Hilsa shad (Tenualosa ilisha), a widely distributed migratory fish, contributes substantially to the economy of Bangladesh. The harvest of hilsa from inland waters has been fluctuating due to anthropological and climate change-induced degradation of the riverine habitats. The whole genome sequence of this valuable fish could provide genomic tools for sustainable harvest, conservation and productivity cycle maintenance. Here, we report the first draft genome of T. ilisha from the Bay of Bengal, the largest reservoir of the migratory fish. Methods: A live specimen of T. ilisha was collected from the Bay of Bengal. The whole genome sequencing was performed by the Illumina HiSeqX platform (2 × 150 paired end configuration). We assembled the short reads using SOAPdenovo2 genome assembler and predicted protein coding genes by AUGUSTUS. The completeness of the T. ilisha genome assembly was evaluated by BUSCO (Benchmarking Universal Single Copy Orthologs). We identified single nucleotide polymorphisms (SNPs) by calling them directly from unassembled sequence reads using discoSnp++. Results: We assembled the draft genome of 710.28 Mb having an N50 scaffold length of 64157 bp and GC content of 42.95%. A total of 37,450 protein coding genes were predicted of which 29,339 (78.34%) were annotated with other vertebrate genomes. We also identified 792,939 isolated SNPs with transversion:transition ratio of 1:1.8. The BUSCO evaluation showed 78.1% completeness of this genome. Conclusions: The genomic data generated in this study could be used as a reference to identify genes associated with physiological and ecological adaptations, population connectivity, and migration behaviour of this biologically and economically important anadromous fish species of the Clupeidae family.

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

Gigabyte ◽

10.46471/gigabyte.2 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

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

Amphibian genomes are usually challenging to assemble due to their 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.

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Draft Genome Sequence of “Candidatus Sulcia muelleri” Strain KPTW1 from Kolla paulula, a Vector of Xylella fastidiosa Causing Pierce’s Disease of Grapevine in Taiwan

Microbiology Resource Announcements ◽

10.1128/mra.01347-18 ◽

2019 ◽

Vol 8 (2) ◽

Author(s):

Hsien-Tzung Shih ◽

Chiou-Chu Su ◽

Chung-Jan Chang ◽

Sonia Vargas ◽

Zehan Dai ◽

...

Keyword(s):

Xylella Fastidiosa ◽

Draft Genome ◽

Gc Content ◽

Pierce's Disease ◽

Protein Coding ◽

Content Type ◽

Protein Coding Genes ◽

Pierce’S Disease ◽

A Genome ◽

Rna Genes

The genome of “Candidatus Sulcia muelleri” strain KPTW1 from Kolla paulula, a vector of Xylella fastidiosa that causes Pierce’s disease (PD) of grapevine in Taiwan, was sequenced. The strain has a genome size of 253,942 bp, GC content of 22.7%, 237 predicted protein-coding genes, and 34 RNA genes.

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Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus

F1000Research ◽

10.12688/f1000research.44714.1 ◽

2021 ◽

Vol 10 ◽

pp. 29

Author(s):

Jose De Vega ◽

Iain Donnison ◽

Sarah Dyer ◽

Kerrie Farrar

Keyword(s):

Genome Assembly ◽

Draft Genome ◽

Rna Seq ◽

Protein Coding ◽

Draft Genome Assembly ◽

Protein Coding Genes ◽

Gene Annotations ◽

Northern Latitudes ◽

Miscanthus Sacchariflorus ◽

Genomic Studies

Miscanthus sacchariflorus (Maxim.) Hack. is a highly productive C4 perennial rhizomatous biofuel grass crop. M. sacchariflorus is among the most widely distributed species in the genus, particularly at cold northern latitudes, and is one of the progenitor species of the commercial M. × giganteus genotypes. We generated a 2.54 Gb whole-genome assembly of the diploid M. sacchariflorus cv. “Robustus 297” genotype, which represented ~59% of the expected total genome size. We later anchored this assembly using the chromosomes from the M. sinensis genome to generate a second assembly with improved contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored assemblies, respectively. We estimated our assemblies included ~85% of the M. sacchariflorus genes based on homology and core markers. The utility of the new reference for genomic studies was evidenced by a 99% alignment rate of the RNA-seq reads from the same genotype. The raw data, unanchored and anchored assemblies, and respective gene annotations are publicly available.

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A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource

10.1101/2021.11.19.468211 ◽

2021 ◽

Author(s):

Andre Machado ◽

Andre Gomes-dos-Santos ◽

Miguel Fonseca ◽

Rute da Fonseca ◽

Ana Verissimo ◽

...

Keyword(s):

Genome Assembly ◽

Draft Genome ◽

Single Copy ◽

Medium Size ◽

Chub Mackerel ◽

High Quality ◽

Protein Coding ◽

Draft Genome Assembly ◽

Scomber Colias ◽

A Genome

The Atlantic chub mackerel, Scomber colias Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S. colias, produced with Pacbio HiFi long reads and Illumina Paired-End short reads. The estimated genome size is 814 Mb distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4,19 and 3,34 Mb, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3 % of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this is the fourth high-quality genome assembly within the Order Scombriformes and the first in the genus Scomber.

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Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig

Microbiology Resource Announcements ◽

10.1128/mra.00839-20 ◽

2020 ◽

Vol 9 (34) ◽

Cited By ~ 1

Author(s):

Binghui Zhou ◽

Leonardo Albarracin ◽

Yuki Masumizu ◽

Yuhki Indo ◽

M. Aminul Islam ◽

...

Keyword(s):

Genome Sequence ◽

Intestinal Tract ◽

Draft Genome ◽

Gc Content ◽

Draft Genome Sequence ◽

Illumina Hiseq ◽

Protein Coding ◽

Content Type ◽

Protein Coding Genes ◽

A Genome

ABSTRACT Ligilactobacillus salivarius FFIG58 was isolated from the intestine of a wakame-fed pig and sequenced with an Illumina HiSeq system. FFIG58 genome sequencing revealed a genome size of 1,984,180 bp, with 1,994 protein-coding genes and a GC content of 32.9%. This draft genome sequence will contribute to a better understanding of the porcine gut microbiome.

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Draft Genome Sequence of Janthinobacterium sp. Strain ROICE36, a Putative Secondary Metabolite-Synthesizing Bacterium Isolated from Antarctic Snow

Genome Announcements ◽

10.1128/genomea.01553-17 ◽

2018 ◽

Vol 6 (15) ◽

pp. e01553-17 ◽

Cited By ~ 1

Author(s):

Cecilia Chiriac ◽

Andreea Baricz ◽

Cristian Coman

Keyword(s):

Genome Assembly ◽

Genome Analysis ◽

Draft Genome ◽

Gene Clusters ◽

Protein Coding ◽

Content Type ◽

Draft Genome Assembly ◽

Protein Coding Genes ◽

Peptide Synthetase ◽

Antarctic Snow

ABSTRACT The draft genome assembly of Janthinobacterium sp. strain ROICE36 has 207 contigs, with a total genome size of 5,977,006 bp and a G+C content of 62%. Preliminary genome analysis identified 5,363 protein-coding genes and a total of 7 secondary metabolic gene clusters (encoding bacteriocins, nonribosomal peptide-synthetase [NRPS], terpene, hserlactone, and other ketide synthases).

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

10.1101/2021.06.09.447659 ◽

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.

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