scholarly journals Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism

2018 ◽  
Author(s):  
Xiaofeng Dong ◽  
Kittipong Chaisiri ◽  
Dong Xia ◽  
Stuart D. Armstrong ◽  
Yongxiang Fang ◽  
...  
Keyword(s):  
Biological Function ◽  
Scrub Typhus ◽  
Future Research ◽  
Agricultural Pests ◽  
Allergenic Protein ◽  
Draft Assembly ◽  
Mate Pair ◽  
Terpene Synthesis ◽  
Carotenoid Synthesis ◽  
Mate Pair Library

AbstractBackgroundTrombidid mites have a unique lifecycle in which only the larval stage is ectoparasitic. In the superfamily Trombiculoidea (“chiggers”), the larvae feed preferentially on vertebrates, including humans. Species in the genusLeptotrombidiumare vectors of a potentially fatal bacterial infection, scrub typhus, which affects 1 million people annually. Moreover, chiggers can cause pruritic dermatitis (trombiculiasis) in humans and domesticated animals. In the Trombidioidea (velvet mites), the larvae feed on other arthropods and are potential biological control agents for agricultural pests. Here, we present the first trombidid mites genomes, obtained both for a chigger,Leptotrombidium deliense, and for a velvet mite,Dinothrombium tinctorium.ResultsSequencing was performed using Illumina technology. A 180 Mb draft assembly forD. tinctoriumwas generated from two paired-end and one mate-pair library using a single adult specimen. ForL. deliense, a lower-coverage draft assembly (117 Mb) was obtained using pooled, engorged larvae with a single paired-end library. Remarkably, both genomes exhibited evidence of ancient lateral gene transfer from soil-derived bacteria or fungi. The transferred genes confer functions that are rare in animals, including terpene and carotenoid synthesis. Thirty-seven allergenic protein families were predicted in theL. deliensegenome, of which nine were unique. Preliminary proteomic analyses identified several of these putative allergens in larvae.ConclusionsTrombidid mite genomes appear to be more dynamic than those of other acariform mites. A priority for future research is to determine the biological function of terpene synthesis in this taxon and its potential for exploitation in disease control.

scholarly journals Diversidade e sazonalidade de coccinelídeos (Coleoptera: Coccinellidae) em pomar no município de Ponta Grossa, Paraná

2019 ◽  
Vol 12 (3) ◽  
pp. 108-112
Author(s):  
Bruno Piotrovski Begha ◽  
Jana Magaly Tesserolli de Souza ◽  
Carlos Henrique Antunes ◽  
Julianne Milléo
Keyword(s):  
Local Community ◽  
Harmonia Axyridis ◽  
Fruit Trees ◽  
Climatic Conditions ◽  
Future Research ◽  
Agricultural Pests ◽  
Consequent Reduction ◽  
Prey Aphids ◽  
Harmonia Axyridis Pallas ◽  
Citrus Trees

Resumo. Uma análise sobre a flutuação populacional da entomofauna associada a culturas de interesse econômico pode fornecer subsídios para o manejo integrado de pragas. Dentre os grupos economicamente relevantes podemos citar os coccinelídeos, conhecidos por serem predadores naturais de pragas agrícolas como afídeos. O presente trabalho se faz necessário visto que os Campos Gerais ainda carecem de dados sobre Coccinellidae relacionados a pomares de árvores frutíferas. O estudo foi realizado no pomar do Colégio Agrícola Estadual Augusto Ribas (Ponta Grossa-PR) de julho de 2004 a junho de 2006. As coletas foram feitas usando cada espécie do pomar, sendo elas agrupadas em dois grupos: cítricas e decíduas. Harmonia axyridis (Pallas) foi a espécie mais representativa na amostragem, compreendendo 38,35 % das coletas. as árvores cítricas apresentaram o maior número de insetos totalizando 82,19% da amostragem. É pertinente sugerir que a presença da H. axyridis pode ter afetado a diversidade da comunidade local, sendo ela uma espécie invasora e considerada uma melhor competidora. As árvores cítricas se apresentaram como as mais diversas. Podemos atribuir essa distribuição a maior presença de afídeos nas árvores cítricas, que foram atraídos pelos óleos voláteis secretados por essas plantas. No período final da amostragem houve uma queda populacional, que pode ser atribuída a condições climáticas desfavoráveis, e consequente redução a abundância dos afídeos presa e dos próprios coccinelídeos. Uma maior quantidade de recursos de presa permitiria que mais espécies de joaninhas coexistissem sem competir fortemente. Uma pesquisa futura poderia comparar situação da comunidade, analisando a influência da H. axyridis nas espécies locais.Diversity and seasonality of coccinellids (Coleoptera: Coccinellidae) in an orchard in the city of Ponta Grossa, ParanáAbstract. An analysis of the population fluctuation of entomofauna associated with crops of economic interest can provide subsidies for integrated pest management. Among the economically relevant groups we can mention the Coccinellidae, known to include natural predators of agricultural pests such as aphids. The present work is necessary since Parana's Campos Gerais still lack data on Coccinellidae related to orchards of fruit trees. The study was conducted in the orchard of Augusto Ribas State Agricultural College (Ponta Grossa-PR) from July 2004 to June 2006. Samples were collected from each species of the orchard, grouped into two groups: citrus and deciduous. Harmonia axyridis (Pallas) was the most representative species in the sample, comprising 38.35% of the collections. Citrus trees had the highest number of insects totaling 82.19% of the sample. It is pertinent to suggest that the presence of H. axyridis may have affected the diversity of the local community, being an invasive species and considered a better competitor. The citrus trees presented themselves as the most diverse. We can attribute this contribution to the greater presence of aphids in the citrus trees, which were attracted by the volatile oils secreted by these plants. In the final period of sampling there was a decrease in population size, which can be attributed to unfavorable climatic conditions, and consequent reduction in the abundance of prey aphids and of the coccinellids themselves. A greater amount of prey resources would allow more species of ladybugs to coexist without competing strongly. A future research could compare community situation by analyzing the influence of H. axyridis on local species.

scholarly journals BIMA V3: an aligner customized for mate pair library sequencing

2014 ◽  
Vol 30 (11) ◽  
pp. 1627-1629 ◽  
Author(s):  
Travis M. Drucker ◽  
Sarah H. Johnson ◽  
Stephen J. Murphy ◽  
Kendall W. Cradic ◽  
Terry M. Therneau ◽  
...  
Keyword(s):  
Mate Pair ◽  
Mate Pair Library

Preparation of an 8-kb Mate-Pair Library for Illumina Sequencing

2016 ◽  
Vol 2017 (4) ◽  
pp. pdb.prot094664 ◽  
Author(s):  
Elaine Mardis ◽  
W. Richard McCombie
Keyword(s):  
Illumina Sequencing ◽  
Mate Pair ◽  
Mate Pair Library

scholarly journals Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates: TABLE 1 

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Patricio Jeraldo ◽  
Scott A. Cunningham ◽  
Daniel Quest ◽  
Robert A. Sikkink ◽  
Daniel O’Brien ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Draft Genome ◽  
Clinical Isolates ◽  
Genome Sequences ◽  
Mate Pair ◽  
Sequence Types ◽  
Mate Pair Library

We report on nine draft genomes of Pseudomonas aeruginosa isolates, assembled using a hybrid paired-end and Nextera mate-pair library approach. Eight are of clinical origin, and one is the ATCC 27853 strain. We also report their multilocus sequence types.

scholarly journals Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola

2021 ◽  
Author(s):  
Stephen Byrne ◽  
Maximilian Schughart ◽  
James C Carolan ◽  
Michael Gaffney ◽  
Peter J Thorpe ◽  
...  
Keyword(s):  
Barley Yellow Dwarf Virus ◽  
Sitobion Avenae ◽  
Future Research ◽  
Buchnera Aphidicola ◽  
Protein Coding ◽  
Draft Assembly ◽  
Barley Yellow Dwarf ◽  
Grain Aphid ◽  
Yellow Dwarf Virus ◽  
Insight Into

Abstract The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of Barley Yellow Dwarf Virus (BYDV) leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.

scholarly journals Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing

BioTechniques ◽  
2015 ◽  
Vol 58 (5) ◽  
Author(s):  
Kaori Tatsumi ◽  
Osamu Nishimura ◽  
Kazu Itomi ◽  
Chiharu Tanegashima ◽  
Shigehiro Kuraku
Keyword(s):  
Cost Saving ◽  
Library Preparation ◽  
Mate Pair ◽  
Mate Pair Library

scholarly journals Locust Bacterial Symbionts: An Update

Insects ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 655
Author(s):  
Omer Lavy ◽  
Uri Gophna ◽  
Eran Gefen ◽  
Amir Ayali
Keyword(s):  
Reproductive Organs ◽  
The Other ◽  
Future Research ◽  
Bacterial Symbionts ◽  
Agricultural Pests ◽  
Bacterial Composition ◽  
Current State

As one of the world’s most infamous agricultural pests, locusts have been subjected to many in-depth studies. Their ability at one end of their behavioral spectrum to live as solitary individuals under specific conditions, and at the other end of the spectrum to form swarms of biblical scale, has placed them at the focus of vast research efforts. One important aspect of locust ecology is that of their interactions with the bacteria that reside in and on them. Although this aspect of locust ecology has been little studied relative to the mainstream locust research, these bacteria have been shown both to affect locust immunity and to participate in maintaining swarm integrity through the secretion of attractant volatiles. The interaction between locusts and their bacteria seems, however, to be bi-directional, with the bacteria themselves, as recently shown, being influenced by their host’s swarming tendencies. This seems to be a consequence of the bacterial composition in the locust’s gut, reproductive organs, and integument undergoing change with the change in their host’s behavior. In this review we describe the current state of knowledge of the locust–bacteria interactions (data exists mainly for the desert and the migratory locusts), as well as highlighting some newly-gained understanding; and offer perspectives for future research.

Preparation of a 3-kb Mate-Pair Library for Illumina Sequencing

2016 ◽  
Vol 2017 (4) ◽  
pp. pdb.prot094656 ◽  
Author(s):  
Elaine Mardis ◽  
W. Richard McCombie
Keyword(s):  
Illumina Sequencing ◽  
Mate Pair ◽  
Mate Pair Library

Introduction

2013 ◽  
Author(s):  
Craig M. Powell ◽  
Lisa M. Monteggia
Keyword(s):  
Graduate Students ◽  
Undergraduate Students ◽  
Genetic Basis ◽  
Biological Function ◽  
Gene Mutations ◽  
Psychology Students ◽  
Model Systems ◽  
Future Research

The Autisms: Molecules to Model Systems is designed to introduce the genetic basis for multiple autisms and discuss the gene mutations within the context of their biological function. The text is directed to advanced undergraduate students, graduate students, postdoctoral fellows, psychology students and professionals, psychiatrists, neurologists, and neuroscience researchers alike. It is hoped that readers will be engaged in this emerging field and will be motivated to read further and to cultivate their own understanding and constructs for future research into this enigmatic group of disorders known as the autisms.

scholarly journals The Enigmatic Function of PARP1: From PARylation Activity to PAR Readers

Cells ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 1625 ◽  
Author(s):  
Tatiana Kamaletdinova ◽  
Zahra Fanaei-Kahrani ◽  
Zhao-Qi Wang
Keyword(s):  
Chromatin Remodeling ◽  
Functional Relationship ◽  
Biological Function ◽  
Future Research ◽  
Cellular Processes ◽  
Founding Member ◽  
Damage Response ◽  
New Research ◽  
Relationship Of ◽  
Research Avenue

Poly(ADP-ribosyl)ation (PARylation) is catalysed by poly(ADP-ribose) polymerases (PARPs, also known as ARTDs) and then rapidly removed by degrading enzymes. Poly(ADP-ribose) (PAR) is produced from PARylation and provides a delicate and spatiotemporal interaction scaffold for numerous target proteins. The PARylation system, consisting of PAR synthesizers and erasers and PAR itself and readers, plays diverse roles in the DNA damage response (DDR), DNA repair, transcription, replication, chromatin remodeling, metabolism, and cell death. Despite great efforts by scientists in biochemistry, cell and molecular biology, genetics, and pharmacology over the last five decades, the biology of PARPs and PARylation remains enigmatic. In this review, we summarize the current understanding of the biological function of PARP1 (ARTD1), the founding member of the PARP family, focusing on the inter-dependent or -independent nature of different functional domains of the PARP1 protein. We also discuss the readers of PAR, whose function may transduce signals and coordinate the cellular processes, which has recently emerged as a new research avenue for PARP biology. We aim to provide some perspective on how future research might disentangle the biology of PARylation by dissecting the structural and functional relationship of PARP1, a major effector of the PARPs family.

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