scholarly journals Opposite Polarity Monospore Genome De Novo Sequencing and Comparative Analysis Reveal the Possible Heterothallic Life Cycle of Morchella importuna

2018 ◽  
Vol 19 (9) ◽  
pp. 2525 ◽  
Author(s):  
Wei Liu ◽  
LianFu Chen ◽  
YingLi Cai ◽  
QianQian Zhang ◽  
YinBing Bian
Keyword(s):  
Mating Type ◽  
De Novo ◽  
Physical Map ◽  
Gene Annotation ◽  
Divergence Time ◽  
Enrichment Analysis ◽  
Single Copy ◽  
Opposite Polarity ◽  
De Novo Sequencing ◽  
Edible Fungus

Morchella is a popular edible fungus worldwide due to its rich nutrition and unique flavor. Many research efforts were made on the domestication and cultivation of Morchella all over the world. In recent years, the cultivation of Morchella was successfully commercialized in China. However, the biology is not well understood, which restricts the further development of the morel fungus cultivation industry. In this paper, we performed de novo sequencing and assembly of the genomes of two monospores with a different mating type (M04M24 and M04M26) isolated from the commercially cultivated strain M04. Gene annotation and comparative genome analysis were performed to study differences in CAZyme (Carbohydrate-active enzyme) enzyme content, transcription factors, duplicated sequences, structure of mating type sites, and differences at the gene and functional levels between the two monospore strains of M. importuna. Results showed that the de novo assembled haploid M04M24 and M04M26 genomes were 48.98 and 51.07 Mb, respectively. A complete fine physical map of M. importuna was obtained from genome coverage and gene completeness evaluation. A total of 10,852 and 10,902 common genes and 667 and 868 endemic genes were identified from the two monospore strains, respectively. The Gene Ontology (GO) and KAAS (KEGG Automatic Annotation Serve) enrichment analyses showed that the endemic genes performed different functions. The two monospore strains had 99.22% collinearity with each other, accompanied with certain position and rearrangement events. Analysis of complete mating-type loci revealed that the two monospore M. importuna strains contained an independent mating-type structure and remained conserved in sequence and location. The phylogenetic and divergence time of M. importuna was analyzed at the whole-genome level for the first time. The bifurcation time of morel and tuber was estimated to be 201.14 million years ago (Mya); the two monospore strains with a different mating type represented the evolution of different nuclei, and the single copy homologous genes between them were also different due to a genetic differentiation distance about 0.65 Mya. Compared with truffles, M. importuna had an extension of 28 clusters of orthologous genes (COGs) and a contraction of two COGs. The two different polar nuclei with different degrees of contraction and expansion suggested that they might have undergone different evolutionary processes. The different mating-type structures, together with the functional clustering and enrichment analysis results of the endemic genes of the two different polar nuclei, imply that M. importuna might be a heterothallic fungus and the interaction between the endemic genes may be necessary for its complete life history. Studies on the genome of M. importuna facilitate a better understanding of morel biology and evolution.

scholarly journals EnTAP: Bringing Faster and Smarter Functional Annotation to Non-Model Eukaryotic Transcriptomes

2018 ◽  
Author(s):  
Alexander J. Hart ◽  
Samuel Ginzburg ◽  
Muyang (Sam) Xu ◽  
Cera R. Fisher ◽  
Nasim Rahmatpour ◽  
...  
Keyword(s):  
Similarity Search ◽  
De Novo ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
Orthologous Gene ◽  
Protein Domain ◽  
Family Assessment ◽  
Ontology Term ◽  
Protein Coding ◽  
Functional Gene Annotation

ABSTRACTEnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates, while focusing primarily on protein-coding transcripts. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally annotate the translated proteins. Downstream features include fast similarity search across three repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.

scholarly journals The First Draft Genome Assembly of Snow Sheep (Ovis nivicola)

2020 ◽  
Vol 12 (8) ◽  
pp. 1330-1336 ◽  
Author(s):  
Maulik Upadhyay ◽  
Andreas Hauser ◽  
Elisabeth Kunz ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Single Copy ◽  
Climatic Conditions ◽  
Draft Genome Assembly ◽  
Sheep Genome ◽  
Long Reads

Abstract The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (∼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.

scholarly journals Transcriptome sequencing and drought resistance gene annotation in Quercus liaotungensis leaves

2021 ◽  
Vol 43 (8) ◽  
Author(s):  
Guobao Wang ◽  
Li Qin
Keyword(s):  
Candidate Genes ◽  
Drought Resistance ◽  
De Novo ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Sequencing Platform ◽  
Drought Avoidance ◽  
Transcriptomic Sequencing ◽  
Genes Encoding

AbstractQ. liaotungensis is an important drought-resistant tree species in Northeast China where the climate is dry and rainless. In this study, we performed a deep transcriptomic sequencing in Q. liaotungensis leaves, including de novo assembly and functional annotation for screening the candidate genes involved in drought avoidance. A total of 25,593 unigenes were obtained from Illumina sequencing platform. According to Gene Ontology annotation and KEGG pathway enrichment analysis, we screened a series of candidate genes encoding SOD, POD, CAT, DREB, MYB, WRKY, bZIP, and NAC from the Q. liaotungensis leaf transcriptome, all of which are potentially involved in drought resistance. The results of this study expanded the genetic resources of Q. liaotungensis and provided a theoretical basis for further exploring the functional gene information of Q. liaotungensis.

scholarly journals Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage

2021 ◽  
Author(s):  
Kameron T Wittmeyer ◽  
Sara J Oppenheim ◽  
Keith R Hopper
Keyword(s):  
De Novo Assembly ◽  
Genetic Linkage ◽  
De Novo ◽  
Gene Annotation ◽  
Chromosomal Rearrangements ◽  
Single Copy ◽  
Linkage Data ◽  
Modest Improvement ◽  
Functional Annotations ◽  
Aphid Parasitoids

Abstract Safe, effective biological-control introductions against invasive pests depend on narrowly host-specific natural enemies with the ability to adapt to a changing environment. As part of a project on the genetic architectures of these traits, we assembled and annotated the genomes of two aphid parasitoids, Aphelinus atriplicis and Aphelinus certus. We report here several assemblies of A. atriplicis made with Illumina and PacBio data, which we combined into a meta-assembly. We scaffolded the meta-assembly with markers from a genetic map of hybrids between A. atriplicis and A. certus. We used this genetic-linkage scaffolded (GLS) assembly of A. atriplicis to scaffold a de novo assembly of A. certus. The de novo assemblies of A. atriplicis differed in contiguity, and the meta-assembly of these assemblies was more contiguous than the best de novo assembly. Scaffolding with genetic-linkage data allowed chromosomal-level assembly of the A. atriplicis genome and scaffolding a de novo assembly of A. certus with this GLS assembly, greatly increased the contiguity of the A. certus assembly to the point where it was also at the chromosomal-level. However, completeness of the A. atriplicis assembly, as measured by % complete, single-copy BUSCO hymenopteran genes, varied little among de novo assemblies and was not increased by meta-assembly or genetic scaffolding. Furthermore, the greater contiguity of the meta-assembly and GLS assembly had little or no effect on the numbers of genes identified, the proportion with homologs or functional annotations. Increased contiguity of the A. certus assembly provided modest improvement in assembly completeness, as measured by % complete, single-copy BUSCO hymenopteran genes. The total genic sequence increased, and while the number of genes declined, gene length increased, which together suggest greater accuracy of gene models. More contiguous assemblies provide uses other than gene annotation, for example, identifying the genes associated with quantitative trait loci and understanding of chromosomal rearrangements associated with speciation.

scholarly journals Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C

GigaScience ◽  
2020 ◽  
Vol 9 (4) ◽  
Author(s):  
Matt A Field ◽  
Benjamin D Rosen ◽  
Olga Dudchenko ◽  
Eva K F Chan ◽  
Andre E Minoche ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Draft Genome ◽  
Single Copy ◽  
Canis Lupus Familiaris ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
First Choice

Abstract Background The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. Findings Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. Conclusions GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.

scholarly journals De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure

2021 ◽  
Author(s):  
John Martinson ◽  
David C. Bencic ◽  
Gregory P. Toth ◽  
Mitchell S. Kostich ◽  
Robert W. Flick ◽  
...  
Keyword(s):  
Gene Structure ◽  
Fathead Minnow ◽  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Pimephales Promelas ◽  
Single Copy ◽  
Model Organisms ◽  
Coding Regions ◽  
Genomic Resource

ABSTRACTThe Fathead Minnow (FHM) is one of the most important and widely used model organisms in aquatic toxicology. The lack of a high-quality and well-annotated FHM reference genome, however, has severely hampered the efforts using modem ‘omics approaches with FHM for environmental toxicogenomics studies. We present here a de novo assembled and nearly complete reference of the fathead minnow genome. Compared to the current fragmented and sparsely annotated FHM genome assembly (FHM1), the new highly contiguous and well-annotated FHM reference genome (FHM2) represents a major improvement, having 95.1% of the complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) and a scaffold N50 of 12.0 Mbps. The completeness of gene annotation for the FHM2 reference genome was demonstrated to be comparable to that of the zebrafish (ZF) GRCz11 reference genome. In addition, our comparative genomics analyses between FHM and ZF revealed highly conserved coding regions between two species while discovering much more compact gene structure in FHM than ZF. This study not only provides insights for assembling a highly repetitive AT-rich genome, but also delivers a critical genomic resource essential for toxicogenomics studies in environmental toxicology.

scholarly journals STRONG: metagenomics strain resolution on assembly graphs

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Christopher Quince ◽  
Sergey Nurk ◽  
Sebastien Raguideau ◽  
Robert James ◽  
Orkun S. Soyer ◽  
...  
Keyword(s):  
Time Series ◽  
De Novo ◽  
Single Copy ◽  
Bayesian Algorithm ◽  
Anaerobic Digestor ◽  
Core Genes

AbstractWe introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.

scholarly journals Complete chloroplast genome of Alternanthera philoxeroides by de novo sequencing

2021 ◽  
Vol 6 (7) ◽  
pp. 1826-1828
Author(s):  
Ping Jiang ◽  
Guangpei Xu ◽  
Yanfei He ◽  
Taotao Sun ◽  
Changli Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
De Novo Sequencing ◽  
Alternanthera Philoxeroides ◽  
Complete Chloroplast Genome

scholarly journals Multiple Chromosomes in Bacteria: The Yin and Yang of trp Gene Localization in Rhodobacter sphaeroides 2.4.1

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 525-538
Author(s):  
Chris Mackenzie ◽  
Adrian E Simmons ◽  
Samuel Kaplan
Keyword(s):  
Rhodobacter Sphaeroides ◽  
Biosynthetic Pathway ◽  
Southern Blotting ◽  
Physical Map ◽  
Functional Integration ◽  
Bacterial Genome ◽  
Single Copy ◽  
Gene Localization ◽  
Yin And Yang ◽  
Trp Genes

Abstract The existence of multiple chromosomes in bacteria has been known for some time. Yet the extent of functional solidarity between different chromosomes remains unknown. To examine this question, we have surveyed the well-described genes of the tryptophan biosynthetic pathway in the multichromosomal photosynthetic eubacterium Rhodobacter sphaeroides 2.4.1. The genome of this organism was mutagenized using Tn5, and strains that were auxotrophic for tryptophan (Trp-) were isolated. Pulsed-field gel mapping indicated that Tn5 insertions in both the large (3 Mb CI) and the small (0.9 Mb CII) chromosomes created a Trp- phenotype. Sequencing the DNA flanking the sites of the Tn5 insertions indicated that the genes trpE-yibQ-trpGDC were at a locus on CI, while genes trpF-aroR-trpB were at locus on CII. Unexpectedly, trpA was not found downstream of trpB. Instead, it was placed on the CI physical map at a locus 1.23 Mb away from trpE-yibQ-trpGDC. To relate the context of the R. sphaeroides trp genes to those of other bacteria, the DNA regions surrounding the trp genes on both chromosomes were sequenced. Of particular significance was the finding that rpsA1, which encodes ribosomal protein S1, and cmkA, which encodes cytidylate monophosphate kinase, were on CII. These genes are considered essential for translation and chromosome replication, respectively. Southern blotting suggested that the trp genes and rpsA1 exist in single copy within the genome. To date, this topological organization of the trp “operon” is unique within a bacterial genome. When taken with the finding that CII encodes essential housekeeping functions, the overall impression is one of close regulatory and functional integration between these chromosomes.

scholarly journals De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma

2021 ◽  
Author(s):  
Mathieu Dupré ◽  
Magalie Duchateau ◽  
Rebecca Sternke-Hoffmann ◽  
Amelie Boquoi ◽  
Christian Malosse ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Light Chain ◽  
De Novo ◽  
De Novo Sequencing
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