Genomes of Diptera

Wiegmann, Brian M.; Richards, Stephen

doi:10.1016/j.cois.2018.01.007

Cited by 26 publications

(18 citation statements)

References 92 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Additionally, many species are sequenced in the course of advancing basic research, often in the area of ecological and evolutionary studies. The progress of insect genome sequencing has been recently reviewed for several well‐studied insect groups, including beetles (McKenna, ), dipterans (Wiegmann and Richards, ), hymenopterans (Branstetter et al ., ) and lepidopterans (Triant et al ., ), The genomic features, and new insights into the interesting physiological traits of these groups were presented in these reviews. In contrast, we herein provide an overview of basic characteristics of all annotated insect genomes currently available, presenting a whole picture of insect genome sequencing.…”

Section: Genomes Of Prominent Insects: Model Medical and Agriculturamentioning

confidence: 99%

Insect genomes: progress and challenges

Zhao

et al. 2019

Insect Molecular Biology

136

View full text Add to dashboard Cite

In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome‐sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein‐coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well‐studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data‐mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.

show abstract

Section: Genomes Of Prominent Insects: Model Medical and Agriculturamentioning

confidence: 99%

Insect genomes: progress and challenges

Zhao

et al. 2019

Insect Molecular Biology

136

View full text Add to dashboard Cite

show abstract

“…Diptera (true flies) are the most abundant and diversified endopterygota (or holometabola) of the insect order, with more than 180 families of about 158,000 described species 1 , 2 . ‘Filth flies’ (diptera) are universal, ubiquitous, coprophagic and synanthropic (living in close association with humans) insects that breed in garbage, animal and human faeces 3 .…”

Section: Introductionmentioning

confidence: 99%

“…https://doi.org/10.1038/s41598-020-74112-x www.nature.com/scientificreports/ResultsSampling sites. In total, 109 sites were sampled, with a total area cover of 15,075,000 m2 (Fig. 1).…”

mentioning

confidence: 99%

Antimicrobial resistant and enteropathogenic bacteria in ‘filth flies’: a cross-sectional study from Nigeria

Onwugamba

Mellmann

Nwaugo

et al. 2020

Sci Rep

View full text Add to dashboard Cite

‘Filth flies’ facilitate the dispersal of pathogens between animals and humans. The objective was to study the intestinal colonization with antimicrobial resistant and enteropathogenic bacteria in ‘filth flies’ from Nigeria. Flies from Southern Nigeria were screened for extended-spectrum β-lactamase producing Enterobacterales (ESBL-E), Staphylococcus aureus, Salmonella sp., Shigella sp., Campylobacter sp. and Yersinia enterocolitica by culture. ESBL-E were tested for blaSHV, blaCTX-M and blaTEM; S. aureus was screened for enterotoxins. Spa typing and multilocus sequence typing (MLST) was done for S. aureus and MLST for Escherichia coli. Of 2,000 flies, 400 were randomly collected for species identification. The most common species were Musca domestica (44.8%, 179/400), Chrysomya putoria (21.6%, 85/400) and Musca sorbens (18.8%, 75/400). Flies were colonized with S. aureus (13.8%, 275/2,000) and ESBL-E (0.8%, 16/2,000). No other enteropathogenic bacteria were detected. The enterotoxin sei was most common (26%, 70/275) in S. aureus, followed by sea (12%, n = 32/275). Four S. aureus isolates were methicillin resistant (mecA positive, t674 and t5305, ST15). The blaCTX-M (n = 16) was the most prevalent ESBL subtype, followed by blaTEM (n = 8). ‘Filth flies’ can carry antimicrobial resistant bacteria in Nigeria. Enterotoxin-positive S. aureus might be the main reason for food poisoning by ‘filth flies’ in the study area.

show abstract

“…Such a variation in TE content may be the reflection of variation in epigenetic regulation at work in these related species. In other more distantly related Diptera, for which more than one hundred genomes have been sequenced to date [38], the amount of TEs may also be very variable and sometimes much larger than what is observed in D. melanogaster , generally associated with larger genome sizes. This is the case for example for the southern house mosquito Culex quinquefasciatus (genome size of 579 Mbp) [39], the mosquito Aedes aegypti (genome size of 1.38 Gbp) [40], and the tiger mosquito A. albopictus (genome size of 1.97 Gbp) [41].…”

Section: Examples Of the Importance Of Tes In Epigenomic Analyses mentioning

confidence: 99%

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Lerat

Casacuberta

Chaparro

et al. 2019

Genes

View full text Add to dashboard Cite

Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.

show abstract

Genomes of Diptera

Cited by 26 publications

References 92 publications

Insect genomes: progress and challenges

Insect genomes: progress and challenges

Antimicrobial resistant and enteropathogenic bacteria in ‘filth flies’: a cross-sectional study from Nigeria

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Contact Info

Product

Resources

About