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 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 Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 289
Author(s):  
Xiao Ma ◽  
Jeanine L. Olsen ◽  
Thorsten B.H. Reusch ◽  
Gabriele Procaccini ◽  
Dave Kudrna ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Zostera Marina ◽  
Draft Genome ◽  
High Molecular Weight Dna ◽  
Protein Coding ◽  
New Findings ◽  
Long Read ◽  
Sanger Sequence ◽  
Assembly Pipeline ◽  
Chromosome Level

Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings.   Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding.  Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins.  Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

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 The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 708 ◽  
Author(s):  
Julien Alban Nguinkal ◽  
Ronald Marco Brunner ◽  
Marieke Verleih ◽  
Alexander Rebl ◽  
Lidia de los Ríos-Pérez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Gene Prediction ◽  
Draft Genome ◽  
Single Copy ◽  
Sander Lucioperca ◽  
Illumina Platform ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
And Performance

The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.

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 The draft genome sequence of the grove snail Cepaea nemoralis

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Suzanne V Saenko ◽  
Dick S J Groenenberg ◽  
Angus Davison ◽  
Menno Schilthuizen
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Agricultural Pests ◽  
Shell Color ◽  
Protein Coding ◽  
Cepaea Nemoralis ◽  
Edible Species ◽  
Wide Range ◽  
In Captivity ◽  
Long Read

Abstract Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of “supergenes,” as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.

scholarly journals Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

ABSTRACTThe Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

scholarly journals Draft Genome Sequence of Bacillus marisflavi CK-NBRI-03, Isolated from Agricultural Soil

2020 ◽  
Vol 9 (7) ◽  
Author(s):  
Mayank Gupta ◽  
Puneet Singh Chauhan ◽  
Sudhir K. Sopory ◽  
Sneh L. Singla-Pareek ◽  
Nidhi Adlakha ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Agricultural Soil ◽  
Draft Genome ◽  
Uttar Pradesh ◽  
Draft Genome Sequence ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Content Type ◽  
Draft Genome Assembly

Here, we report the 4.34-Mb draft genome assembly of Bacillus marisflavi CK-NBRI-03 (or P3), a Gram-positive bacterium, with an average G+C content of 48.66%. P3 was isolated from agricultural soil from the Badaun (midwestern plain zone) region of Uttar Pradesh, India.

scholarly journals Draft Genome Sequence ofBacillus subtilisIa1a, a New Strain for Poly-γ-Glutamic Acid and Exopolysaccharide Production

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Mohammad H. A. Ibrahim ◽  
Brady F. Cress ◽  
Robert J. Linhardt ◽  
Mattheos A. G. Koffas ◽  
Richard A. Gross
Keyword(s):  
Bacillus Subtilis ◽  
Glutamic Acid ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Carbon Sources ◽  
Draft Genome Sequence ◽  
High Quality ◽  
Exopolysaccharide Production ◽  
Draft Genome Assembly

We report here the 4.092-Mb high-quality draft genome assembly of a newly isolated poly-γ-glutamic acid–producing strain,Bacillus subtilisIa1a. The genome sequence is considered a critical tool to facilitate the engineering of improved production strains. Exopolysaccharides and many industrially important enzymes can be produced by this new strain utilizing different carbon sources.

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.

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