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.

De novo assembly, gene annotation, and marker development using Illumina paired-end transcriptome sequencing in the Crassadoma gigantea

Gene ◽  
2018 ◽  
Vol 658 ◽  
pp. 54-62 ◽  
Author(s):  
Shanmao Cao ◽  
Lijie Zhu ◽  
Hongtao Nie ◽  
Minghao Yin ◽  
Gang Liu ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Gene Annotation ◽  
Marker Development

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.

De novo assembly and functional annotations of the transcriptome of Metorchis orientalis (trematoda: Opisthorchiidae)

2018 ◽  
Vol 184 ◽  
pp. 90-96 ◽  
Author(s):  
Jun-Feng Gao ◽  
Yuan Gao ◽  
Jian-Hua Qiu ◽  
Qiao-cheng Chang ◽  
Yan Zhang ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Functional Annotations

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 De Novo Assembly Discovered Novel Structures in Genome of Plastids and Revealed Divergent Inverted Repeats in Mammillaria (Cactaceae, Caryophyllales)

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 392 ◽  
Author(s):  
Solórzano ◽  
Chincoya ◽  
Sanchez-Flores ◽  
Estrada ◽  
Díaz-Velásquez ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Intergenic Spacer ◽  
Structural Diversity ◽  
Single Copy ◽  
Complete Sequence ◽  
Inverted Repeats ◽  
Total Size ◽  
Composition Structure ◽  
Novel Structures

The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.5 to 10 times larger than the small single copy (SSC), and two IRs that contain strong differences in length and gene composition. Structure 1 is distinguished by short IRs of <1 kb composed by rpl23-trnI-CAU-ycf2; with a total length of 110,189 bp and 113 genes. In structure 2, each IR is approximately 7.2 kb and is composed of 11 genes and one Intergenic Spacer-(psbK-trnQ)-trnQ-UUG-rps16-trnK-UUU-matK-trnK-UUU-psbA-trnH-GUG-rpl2-rpl23-trnI-CAU-ycf2; with a total size of 116,175 bp and 120 genes. Structure 3 has divergent IRs of approximately 14.1 kb, where IRA is composed of 20 genes: psbA-trnH-GUG-rpl23-trnI-CAU-ycf2-ndhB-rps7-rps12-trnV-GAC-rrn16-ycf68-trnI-GAU-trnA-AGC-rrn23-rrn4.5-rrn5-trnR-ACG-trnN-GUU-ndhF-rpl32; and IRB is identical to the IRA, but lacks rpl23. This structure has 131 genes and, by pseudogenization, it is shown to have the shortest cpDNA, of just 107,343 bp. Our findings show that Mammillaria bears an unusual structural diversity of cpDNA, which supports the elucidation of the evolutionary processes involved in cacti lineages.

scholarly journals A new experimental system to study meiotic recurrent non-allelic homologous recombination in budding yeast

2020 ◽  
Author(s):  
Hailey N. C. Sedam ◽  
Juan Lucas Argueso
Keyword(s):  
Homologous Recombination ◽  
Copy Number ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Experimental System ◽  
Single Copy ◽  
Copy Number Variations ◽  
Repeat Elements ◽  
Promising Tool ◽  
Recombination Pathway

ABSTRACTIn humans, de novo recurrent copy number variations (CNVs) often arise during meiosis from non-allelic homologous recombination (NAHR) between low copy repeat elements (LCRs). These chromosomal rearrangements are responsible for a wide variety of genomic disorders involving duplication or deletion of dose-sensitive genes. The precise factors that steer meiotic cells toward this detrimental recombination pathway are not fully understood. To create a model for the investigation of LCR-mediated CNV mechanisms, we developed a diploid experimental system in Saccharomyces cerevisiae. We modified the right arm of chromosome V through the introduction of engineered LCRs: duplicated 5 to 35 kb segments of yeast DNA flanking single copy interstitial spacers, analogously to the meiotic NAHR substrates that exist in humans. Phenotypic markers, including a copy number reporter, were inserted within the interstitial spacer. Their segregation in the haploid meiotic progeny was used to phenotypically identity and classify recurrent CNV events. This system allowed us to measure the effects of LCR size on the frequency of meiotic de novo recurrent CNV formation, and to determine the relative proportions of each of the three main NAHR classes: interhomolog, intersister, and intrachromatid. The frequency of CNV increased as the LCRs became larger, and interhomolog NAHR was overrepresented relative to the two other classes. We showed that this experimental system directly mimics the features of de novo recurrent CNVs reported in human disease, thus it represents a promising tool for the discovery and characterization of conserved cellular factors and environmental exposures that can modulate meiotic NAHR.

Sign in / Sign up

Export Citation Format

Share Document