scholarly journals A highly contiguous genome assembly of a polyphagous predatory mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae)

2021 ◽  
Author(s):  
Yi Yan ◽  
Na Zhang ◽  
Chenglin Liu ◽  
Xinran Wu ◽  
Kai Liu ◽  
...  
Keyword(s):  
Biological Control ◽  
Genome Assembly ◽  
Evolutionary Biology ◽  
Draft Genome ◽  
Predatory Mite ◽  
Detoxification Enzymes ◽  
Read Length ◽  
Average Read Length ◽  
Predaceous Mites ◽  
Stratiolaelaps Scimitus

Abstract As a polyphagous soil-dwelling predatory mite, Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae), formerly known as Stratiolaelaps miles (Berlese), is native to the Northern hemisphere and preys on soil invertebrates, including fungus gnats, springtails, thrips nymphs, nematodes, and other species of mites. Already mass-produced and commercialized in North America and Europe, S. scimitus is now introduced in China as a biocontrol agent for field crop. The introduction, however, can lead to unexpected genetic changes within populations of biological control agents, which might decrease the efficacy of pest management or increase the risks to local environments. To better understand the genetic basis of its biology and behavior, we sequenced and assembled the draft genome of S. scimitus using the PacBio Sequel platform II. We generated ∼150 × (64.81 Gb) PacBio long reads with an average read length of 12.60 kb. Reads longer than 5 kb were assembled into contigs, resulting in the final assembly of 158 contigs with a N50 length of 7.66 Mb, and captured 93.1% of the BUSCO gene set (n = 1,066). We identified 16.39% (69.91 Mb) repetitive elements, 1,686 non-coding RNAs, and 13,305 protein-coding genes, which represented 95.8% BUSCO completeness. Combining analyses of genome family evolution and function enrichment of gene ontology and pathway, a total of 135 families experienced significant expansions, which were mainly involved in digestion, detoxification, immunity and venom. Major expansions of the detoxification enzymes, i.e., P450s and carboxylesterases, suggest a possible genetic mechanism underlying polyphagy and ecological adaptions. Our high-quality genome assembly and annotation provide new insights on the evolutionary biology, soil ecology and biological control for predaceous mites.

scholarly journals A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Martin Pippel ◽  
David Jebb ◽  
Franziska Patzold ◽  
Sylke Winkler ◽  
Heiko Vogel ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Annotation ◽  
Incomplete Lineage Sorting ◽  
Read Length ◽  
Ecological Niches ◽  
Average Read Length ◽  
General Applicability ◽  
Pacific Biosciences ◽  
A Genome ◽  
Wide Range

Abstract Background Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. Results Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. Conclusions Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.

Lethal and Sub-Lethal Effects of Novaluron (Pedestal®) on the Soil-Dwelling Predatory Mite, Stratiolaelaps scimitus (Womersley) (Acari: Mesostigmata: Laelapidae), under Laboratory Conditions

2005 ◽  
Vol 40 (1) ◽  
pp. 47-53 ◽  
Author(s):  
Ana R. Cabrera ◽  
Raymond A. Cloyd ◽  
Edmond R. Zaborski
Keyword(s):  
Biological Control ◽  
Growth Regulator ◽  
Harmful Effect ◽  
Predatory Mite ◽  
Insect Growth Regulator ◽  
Water Control ◽  
Lethal Effects ◽  
Insect Growth ◽  
Fungus Gnats ◽  
Stratiolaelaps Scimitus

Laboratory experiments were conducted to determine the lethal and sub-lethal effects of the insect growth regulator, novaluron, on Stratiolaelaps scimitus (Womersley), a soil-dwelling predatory mite widely marketed in North America as Hypoaspis miles (Berlese) for biological control of dark-winged fungus gnats (Bradysia spp.). The lethal effects of novaluron and dicofol were determined at 24, 48 and 72 h. Fifty S. scimitus protonymphs were used for each treatment. Novaluron was applied at a concentration of 62 ml per liter and dicofol was applied at 171 mg per liter. In the sublethal effect experiment, 15 S. scimitus protonymphs were exposed to water and novaluron for 72 h. Novaluron did not have any harmful effect on S. scimitus protonymphs (0% mortality) after 72 h of exposure. Dicofol, as the positive control, caused 58, 98 and 100% mortality of S. scimitus protonymphs after 24, 48 and 72 h of exposure, respectively. After 72 h of exposure, novaluron significantly prolonged the duration of the protonymphal stage by 1 to 2 d, compared to the water control. However, after the mites had molted to the deutonymphal stage, no significant effect on the duration of this stage was observed. This study presents new research on the compatibility of the insect growth regulator, novaluron, with a different mite species. As a result, greenhouse producers can use novaluron to manage plant-feeding insects without disrupting biological control programs for fungus gnats.

scholarly journals The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Weiwen Wang ◽  
Ashutosh Das ◽  
David Kainer ◽  
Miriam Schalamun ◽  
Alejandro Morales-Suarez ◽  
...  
Keyword(s):  
Error Rate ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Nuclear Genome ◽  
Read Length ◽  
High Coverage ◽  
Ecological Importance ◽  
Validation Set

Abstract Background Eucalyptus pauciflora (the snow gum) is a long-lived tree with high economic and ecological importance. Currently, little genomic information for E. pauciflora is available. Here, we sequentially assemble the genome of Eucalyptus pauciflora with different methods, and combine multiple existing and novel approaches to help to select the best genome assembly. Findings We generated high coverage of long- (Nanopore, 174×) and short- (Illumina, 228×) read data from a single E. pauciflora individual and compared assemblies from 5 assemblers (Canu, SMARTdenovo, Flye, Marvel, and MaSuRCA) with different read lengths (1 and 35 kb minimum read length). A key component of our approach is to keep a randomly selected collection of ∼10% of both long and short reads separated from the assemblies to use as a validation set for assessing assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in 8 ways: contig N50, BUSCO scores, LAI (long terminal repeat assembly index) scores, assembly ploidy, base-level error rate, CGAL (computing genome assembly likelihoods) scores, structural variation, and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ∼0.006 errors per base. Conclusions We report a draft genome of E. pauciflora, which will be a valuable resource for further genomic studies of eucalypts. The approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies from a single dataset.

scholarly journals Draft Genome Sequence of a Fungus (Fusarium tricinctum) Cultured from a Monoisolate Native to the Himalayas

2018 ◽  
Vol 6 (20) ◽  
Author(s):  
Narendra Meena ◽  
M. Vasundhara ◽  
M. Sudhakara Reddy ◽  
Prashanth Suravajhala ◽  
U. S. Raghavender ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Read Length ◽  
Content Type ◽  
Genome Sequence Assembly ◽  
Sequencing Chemistry ◽  
Fusarium Tricinctum

ABSTRACT Here, we report the draft de novo genome sequence assembly of Fusarium tricinctum (strain T6), using IonTorrent sequencing chemistry and an Ion 530 chip ExT kit for sequencing. The genome assembly resulted in 42,732,204 bp from a total 6.62 Gb, with a median read length of 386 bp.

scholarly journals Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Bhavani Manivannan ◽  
Niranjana Mahalingam ◽  
Sudhir Jadhao ◽  
Amrita Mishra ◽  
Pravin Nilawe ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Genome Assembly ◽  
Biofilm Formation ◽  
Draft Genome ◽  
Drug Resistant ◽  
Draft Genome Assembly ◽  
Extensively Drug Resistant ◽  
History Of ◽  
Urinary Tuberculosis

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

2012 ◽  
Vol 71 (6) ◽  
pp. 895-906 ◽  
Author(s):  
Luming Yang ◽  
Dal-Hoe Koo ◽  
Yuhong Li ◽  
Xuejiao Zhang ◽  
Feishi Luan ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Genome Assembly ◽  
Draft Genome ◽  
High Density ◽  
Chromosome Rearrangements ◽  
Draft Genome Assembly

scholarly journals First draft genome of loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish

2021 ◽  
Author(s):  
Zhijin Liu ◽  
Xuekun Qian ◽  
Ziming Wang ◽  
Huamei Wen ◽  
Ling Han ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Eye Development ◽  
Draft Genome ◽  
Evolutionary Process ◽  
Integrated Approach ◽  
Sequencing Data ◽  
Retina Development ◽  
Draft Genome Assembly ◽  
Surface Dwelling

Abstract BcakgroundLoaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for research into the evolution of cavefishes.ResultsHere we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately 515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. We also performed genome re-sequencing of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O. daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype.ConclusionsWe here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).

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