scholarly journals De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

2020 ◽  
Vol 12 (6) ◽  
pp. 905-910 ◽  
Author(s):  
Ruoyu Liu ◽  
Kun Wang ◽  
Jun Liu ◽  
Wenjie Xu ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Metal Ion ◽  
De Novo ◽  
Demographic History ◽  
Gene Families ◽  
Phylogenetic Position ◽  
Cold Seeps ◽  
Nitrogen And Phosphorus ◽  
De Novo Genome Assembly ◽  
A Genome

Abstract Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

scholarly journals Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Pingping Liang ◽  
Hafiz Sohaib Ahmed Saqib ◽  
Xiaomin Ni ◽  
Yingjia Shen
Keyword(s):  
Dna Repair ◽  
Positive Selection ◽  
Single Molecule ◽  
Genome Assembly ◽  
De Novo ◽  
Gene Families ◽  
Comparative Genomic ◽  
De Novo Genome Assembly ◽  
Marine Medaka ◽  
Oryzias Melastigma

Abstract Background Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. Results In this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses. Conclusions The highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.

scholarly journals A high-quality de novo genome assembly from a single parasitoid wasp

2020 ◽  
Author(s):  
Xinhai Ye ◽  
Yi Yang ◽  
Zhaoyang Tian ◽  
Le Xu ◽  
Kaili Yu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Parasitoid Wasp ◽  
Genome Comparison ◽  
Single Individual ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Low Input ◽  
A Genome ◽  
High Level

AbstractSequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines. Although few studies sequenced a single small insect with about 100 ng DNA as input, it may still be challenging for many small organisms to obtain such amount of DNA from a single individual. Here, we use 20 ng DNA as input, and present a high-quality genome assembly for a single haploid male parasitoid wasp (Habrobracon hebetor) using Nanopore and Illumina. Because of the low input DNA, a whole genome amplification (WGA) method is used before sequencing. The assembled genome size is 131.6 Mb with a contig N50 of 1.63 Mb. A total of 99% Benchmarking Universal Single-Copy Orthologs are detected, suggesting the high level of completeness of the genome assembly. Genome comparison between H. hebetor and its relative Bracon brevicornis shows a high-level genome synteny, indicating the genome of H. hebetor is highly accurate and contiguous. Our study provides an example for de novo assembling a genome from ultra-low input DNA, and will be used for sequencing projects of small sized species and rare samples, haploid genomics as well as population genetics of small sized species.

scholarly journals Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing

2019 ◽  
Author(s):  
Zhoutao Chen ◽  
Long Pham ◽  
Tsai-Chin Wu ◽  
Guoya Mo ◽  
Yu Xia ◽  
...  
Keyword(s):  
Long Range ◽  
De Novo ◽  
Low Cost ◽  
Cost Effective ◽  
De Novo Genome Assembly ◽  
Short Read ◽  
Single Tube ◽  
Haplotype Phasing ◽  
A Genome ◽  
Long Read

AbstractLong-range sequencing information is required for haplotype phasing, de novo assembly and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirement. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-Seq™) technology, which enables a low-cost, high-accuracy and high-throughput short-read next generation sequencer to routinely generate over 100 Kb long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcode linked reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate mega-base-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.

scholarly journals Genomic Insights Into Chemosynthetic Symbiosis in a Deep-Sea Hydrothermal Vent Mussel

2022 ◽  
Author(s):  
Kai Zhang ◽  
Yao Xiao ◽  
Jin Sun ◽  
Ting Xu ◽  
Kun Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
Functional Differentiation ◽  
Cold Seeps ◽  
Proteomic Approach ◽  
Immune Related Genes ◽  
Self Protection

Abstract Background Symbiosis with chemosynthetic bacteria has allowed many invertebrates to flourish in ‘extreme’ deep-sea chemosynthesis-based ecosystems, such as hydrothermal vents and cold seeps. Bathymodioline mussels are considered as models of deep-sea animal-bacteria symbiosis, but the diversity of molecular mechanisms governing host-symbiont interactions remains understudied owing to the lack of hologenomes. In this study, we adopted a total hologenome approach in sequencing the hydrothermal vent mussel Bathymodiolus marisindicus and the endosymbiont genomes combined with a transcriptomic and proteomic approach that explore the mechanisms of symbiosis. Results Here, we provide the first coupled mussel-endosymbiont genome assembly. Comparative genome analysis revealed that both Bathymodiolus marisindicus and its endosymbiont reshape their genomes through the expansion of gene families, likely due to chemosymbiotic adaptation. Functional differentiation of host immune-related genes and attributes of symbiont self-protection that likely facilitate the establishment of endosymbiosis. Hologenomic analyses offer new evidence that metabolic complementarity between the host and endosymbionts enables the host to compensate for its inability to synthesize some essential nutrients, and two pathways (digestion of symbionts and molecular leakage of symbionts) that can supply the host with symbiontderived nutrients. Results also showed that bacteriocin and abundant toxins of symbiont may contribute to the defense of the B. marisindicus holobiont. Moreover, an exceptionally large number of anti-virus systems were identified in the B. marisindicus symbiont, which likely work synergistically to efficiently protect their hosts from phage infection, indicating virus-bacteria interactions in intracellular environments of a deepsea vent mussel. Conclusions Our study provides novel insights into the mechanisms of symbiosis enabling deep-sea mussels to successfully colonize the special hydrothermal vent habitats.

scholarly journals De novo chromosome level assembly of the mule deer (Odocoileus hemionus) genome

2021 ◽  
Author(s):  
Sydney Lamb ◽  
Adam M. Taylor ◽  
Tabitha A. Hughes ◽  
Brock R. McMillan ◽  
Randy T. Larsen ◽  
...  
Keyword(s):  
De Novo ◽  
Demographic History ◽  
Large Population ◽  
Mule Deer ◽  
Continuous Distribution ◽  
Odocoileus Hemionus ◽  
Chromosome Length ◽  
Future Research ◽  
A Genome ◽  
Genomic Studies

The mule deer (Odocoileus hemionus) is an ungulate species that ranges from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can help facilitate knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. While mule deer are excellent candidates for population genomic studies because of their large population size, continuous distribution, and diversity of habitat, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C. We also provide a genome annotation and compare demographic histories of the mule deer and white-tail deer using PSMC. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.

scholarly journals De novo genome assembly and functional annotation for Fusarium langsethiae

2021 ◽  
Author(s):  
Ya Zuo ◽  
Carol Verheecke-Vaessen ◽  
Corentin Molitor ◽  
Angel Medina ◽  
Naresh Magan ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Animal Health ◽  
Data Availability ◽  
Effective Control ◽  
Local Alignment ◽  
De Novo Genome Assembly ◽  
Genome Database ◽  
A Genome ◽  
Fusarium Langsethiae

AbstractMotivationFusarium langsethiae is a T-2 and HT-2 mycotoxins producing Fusarium species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies.ResultsThe F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye; producing a genome assembly total length of 59Mb and N50 of 3.51Mb. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene [email protected] availabilityRaw sequence reads and assembled genome can be downloaded from: GenBank under the accession JAFFKB000000000

scholarly journals De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)

2021 ◽  
Author(s):  
Luis J Chueca ◽  
Tilman Schell ◽  
Markus Pfenninger
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Land Snail ◽  
Land Snails ◽  
Agricultural Pests ◽  
De Novo Genome Assembly ◽  
Draft Genome Assembly ◽  
Western Palearctic ◽  
A Genome

Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.

scholarly journals Whole Genome Sequencing and Comparative Genome Analysis of the Halotolerant Deep Sea Black Yeast Hortaea werneckii

Life ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 229
Author(s):  
Orazio Romeo ◽  
Alessia Marchetta ◽  
Domenico Giosa ◽  
Letterio Giuffrè ◽  
Clara Urzì ◽  
...  
Keyword(s):  
Deep Sea ◽  
Genome Duplication ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Fungal Species ◽  
Black Yeast ◽  
Phylogenomic Analysis ◽  
Hortaea Werneckii ◽  
Niche Adaptation ◽  
A Genome

Hortaea werneckii, an extreme halotolerant black yeast in the order of Capnodiales, was recently isolated from different stations and depths in the Mediterranean Sea, where it was shown to be the dominant fungal species. In order to explore the genome characteristics of these Mediterranean isolates, we carried out a de-novo sequencing of the genome of one strain isolated at a depth of 3400 m (MC873) and a re-sequencing of one strain taken from a depth of 2500 m (MC848), whose genome was previously sequenced but was highly fragmented. A comparative phylogenomic analysis with other published H. werneckii genomes was also carried out to investigate the evolution of the strains from the deep sea in this environment. A high level of genome completeness was obtained for both genomes, for which genome duplication and an extensive level of heterozygosity (~4.6%) were observed, supporting the recent hypothesis that a genome duplication caused by intraspecific hybridization occurred in most H. werneckii strains. Phylogenetic analyses showed environmental and/or geographical specificity, suggesting a possible evolutionary adaptation of marine H. werneckii strains to the deep sea environment. We release high-quality genome assemblies from marine H. werneckii strains, which provides additional data for further genomics analysis, including niche adaptation, fitness and evolution studies.

scholarly journals Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 54 ◽  
Author(s):  
Sofiia Kolchanova ◽  
Sergei Kliver ◽  
Aleksei Komissarov ◽  
Pavel Dobrinin ◽  
Gaik Tamazian ◽  
...  
Keyword(s):  
Puerto Rican ◽  
De Novo ◽  
Demographic History ◽  
Model Systems ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
De Novo Genome Assembly ◽  
The Caribbean ◽  
Amazona Vittata ◽  
Puerto Rican Parrot

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.

scholarly journals Genomic Characterization of a Novel Tenericutes Bacterium from Deep-Sea Holothurian Intestine

2020 ◽  
Vol 8 (12) ◽  
pp. 1874
Author(s):  
Fang-Chao Zhu ◽  
Chun-Ang Lian ◽  
Li-Sheng He
Keyword(s):  
Intestinal Microbiota ◽  
Deep Sea ◽  
De Novo ◽  
Draft Genome ◽  
Acid Synthesis ◽  
Essential Amino Acids ◽  
Extracellular Dna ◽  
Phylogenetic Position ◽  
Metagenomic Sequencing ◽  
Amino Acid Synthesis

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and immunity of animals, but little is known about the composition and function of intestinal microbiota in deep-sea invertebrates. In this study, the intestinal microbiota of six holothurian Molpadia musculus were investigated, showing that their midguts were predominantly occupied by Izemoplasmatales bacteria. Using metagenomic sequencing, a draft genome of 1,822,181 bp was successfully recovered. After comparison with phylogenetically related bacteria, genes involved in saccharide usage and de novo nucleotide biosynthesis were reduced. However, a set of genes responsible for extracellular nucleoside utilization and 14 of 20 amino acid synthesis pathways were completely retained. Under oligotrophic condition, the gut-associated bacterium may make use of extracellular DNA for carbon and energy supplement, and may provide essential amino acids to the host. The clustered regularly interspaced short palindromic repeat (CRISPR) and restriction–modification (RM) systems presented in the genome may provide protection against invading viruses. A linear azol(in)e-containing peptide gene cluster for bacteriocin synthesize was also identified, which may inhibit the colonization and growth of harmful bacteria. Known virulence factors were not found by database searching. On the basis of its phylogenetic position and metabolic characteristics, we proposed that the bacterium represented a novel genus and a novel family within the Izemoplasmatales order and suggested it be named “Candidatus Bathyoplasma sp. NZ”. This was the first time describing host-associated Izemoplasmatales.

Sign in / Sign up

Export Citation Format

Share Document