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

Gigabyte ◽  
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.

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 Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

2021 ◽  
Author(s):  
Roger Huerlimann ◽  
Jeff A Cowley ◽  
Nicholas M Wade ◽  
Yinan Wang ◽  
Naga Kasinadhuni ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Protein Coding ◽  
Black Tiger Shrimp ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Tiger Shrimp ◽  
Endogenous Viral Elements

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of conjoined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

scholarly journals The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

2021 ◽  
Author(s):  
Thomas W Woehner ◽  
Ofere Francis Emeriewen ◽  
Alexander Wittenberg ◽  
Harrie Schneiders ◽  
Ilse Vrijenhoek ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Sour Cherry ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Long Read ◽  
Chromosome Level

Background: Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. Finding: The final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) genome sequence of P. fruticosa were calculated. The N50 contig length ranged between 0.3 and 0.5 Mb with the longest contig being ~6 Mb. BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets. Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was ~44 Mb with the longest chromosome being 66.5 Mb. The repeat content was estimated to ~190 Mb (52 %) and 58,880 protein-coding genes were annotated. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences. Conclusion: This is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.

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 of the biofuel grass crop Miscanthus sacchariflorus

F1000Research ◽  
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.

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

2018 ◽  
Vol 6 (15) ◽  
pp. e01553-17 ◽  
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).

scholarly journals A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis

2020 ◽  
Vol 12 (7) ◽  
pp. 1074-1079 ◽  
Author(s):  
Ruihao Shu ◽  
Jihong Zhang ◽  
Qian Meng ◽  
Huan Zhang ◽  
Guiling Zhou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gene Clusters ◽  
Tibet Plateau ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Ophiocordyceps Sinensis ◽  
Homologous Protein ◽  
Genome Features

Abstract Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or “DongChongXiaCao,” is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18.2 Mb. We used RNA-seq and homologous protein sequences to identify 8,916 protein-coding genes in the IOZ07 assembly. Moreover, 63 secondary metabolite gene clusters were identified in the improved assembly. The improved assembly and genome features described in this study will further inform the evolutionary study and resource utilization of Chinese cordyceps.

scholarly journals Draft Genome Sequence and Assembly ofPhotorhabdus heterorhabditisStrain VMG, a Bacterial Symbiont Associated with the Entomopathogenic NematodeHeterorhabditis zealandica

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Stephanie Naidoo ◽  
Boipelo Mothupi ◽  
Jonathan Featherston ◽  
Phelelani T. Mpangase ◽  
Vincent M. Gray
Keyword(s):  
South Africa ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Entomopathogenic Nematode ◽  
Draft Genome ◽  
Bacterial Symbiont ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Protein Coding Genes

Here, we report the draft genome sequence ofPhotorhabdus heterorhabditisstrain VMG, a symbiont of the entomopathogenic nematodeHeterorhabditis zealandicain South Africa. The draft genome sequence is 4,878,919 bp long and contains 4,023 protein-coding genes. The genome assembly contains 262 contigs with a G+C content of 42.22%.

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 Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica

2020 ◽  
Vol 9 (14) ◽  
Author(s):  
Claudia Coleine ◽  
Sawyer Masonjones ◽  
Silvano Onofri ◽  
Laura Selbmann ◽  
Jason E. Stajich
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Basidiomycetous Yeast ◽  
Draft Genome Sequence ◽  
Polar Regions ◽  
Dry Valleys ◽  
Antarctic Soil ◽  
Protein Coding ◽  
Protein Coding Genes

A draft genome sequence was assembled and annotated of the basidiomycetous yeast Rhodotorula sp. strain CCFEE 5036, isolated from Antarctic soil communities. The genome assembly is 19.07 megabases and encodes 6,434 protein-coding genes. The sequence will contribute to understanding the diversity of fungi inhabiting polar regions.

Sign in / Sign up

Export Citation Format

Share Document