scholarly journals Distribution of Genes and Repetitive Elements in theDiabrotica virgifera virgiferaGenome Estimated Using BAC Sequencing

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Brad S. Coates ◽  
Analiza P. Alves ◽  
Haichuan Wang ◽  
Kimberly K. O. Walden ◽  
B. Wade French ◽  
...  
Keyword(s):  
Bac Library ◽  
Diabrotica Virgifera Virgifera ◽  
Diabrotica Virgifera ◽  
Genome Coverage ◽  
Haplotype Variation ◽  
Endogenous Genes ◽  
Evolution Of Resistance ◽  
Haploid Genome Size ◽  
Corn Plants ◽  
Paired End Sequencing

Feeding damage caused by the western corn rootworm,Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with104±34.5 kb inserts was created, which has an~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage) and indicated~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that theD. virgifera virgiferagenome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding.

Diabrotica virgifera virgifera. [Distribution map].

2012 ◽  
Author(s):  
Keyword(s):  
New York ◽  
North Carolina ◽  
South Dakota ◽  
Rhode Island ◽  
New Hampshire ◽  
Diabrotica Virgifera Virgifera ◽  
Diabrotica Virgifera ◽  
Distribution Map ◽  
New Distribution ◽  
Distribution In Europe

Abstract A new distribution map is provided for Diabrotica virgifera virgifera LeConte. Coleoptera: Chrysomelidae. Hosts: maize (Zea mays). Information is given on the geographical distribution in Europe (Albania, Austria, Belarus, Belgium, Bosnia-Hercegovina, Bulgaria, Croatia, Czech Republic, France, Germany, Greece, Hungary, Italy, Montenegro, Netherlands, Poland, Romania, Russia, Serbia, Slovakia, Switzerland, UK (England and Wales), Ukraine, Canada (Ontario, Quebec), Mexico, USA (Alabama, Arizona, Colorado, Connecticut, Delaware, Georgia, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Massachusetts, Michigan, Minnesota, Missouri, Montana, Nebraska, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Pennsylvania, Rhode Island, South Dakota, Texas, Utah, Virginia, Washington, West Virginia, Wisconsin, Wyoming)), Central America & Caribbean (Costa Rica, Guatemala, Nicaragua).

scholarly journals Detection of alternative splicing in Diabrotica virgifera virgifera LeConte, in association with Bt resistance using RNA-seq and PacBio Iso-Seq

2020 ◽  
Author(s):  
Zixiao Zhao ◽  
Christine G. Elsik ◽  
Bruce E. Hibbard ◽  
Kent S. Shelby
Keyword(s):  
Alternative Splicing ◽  
Matrix Protein ◽  
Diabrotica Virgifera Virgifera ◽  
Western Corn Rootworm ◽  
Corn Rootworm ◽  
Diabrotica Virgifera ◽  
Rna Seq ◽  
Bt Resistance ◽  
Bt Toxins ◽  
Alternatively Spliced

AbstractBackgroundAlternative splicing is one of the major mechanisms that increases transcriptome diversity in eukaryotes, including insect species that have gained resistance to pesticides and Bt toxins. In western corn rootworm (Diabrotica virgifera virgifera LeConte), neither alternative splicing nor its role in resistance to Bt toxins has been studied.ResultsTo investigate the mechanisms of Bt resistance we carried out single-molecule real-time (SMRT) transcript sequencing and Iso-seq analysis on resistant, eCry3.1Ab-selected and susceptible, unselected, western corn rootworm neonate midguts which fed on seedling maize with and without eCry3.1Ab for 12 and 24 hours. We present transcriptome-wide alternative splicing patterns of western corn rootworm midgut in response to feeding on eCry3.1Ab-expressing corn using a comprehensive approach that combines both RNA-seq and SMRT transcript sequencing techniques. We found that 67.73% of multi-exon genes are alternatively spliced, which is consistent with the high transposable element content of the genome. One of the alternative splicing events we identified was a novel peritrophic matrix protein with two alternative splicing isoforms. Analysis of differential exon usage between resistant and susceptible colonies showed that in eCry3.1Ab-resistant western corn rootworm, expression of one isoform was significantly higher than in the susceptible colony, while no significant differences between colonies were observed with the other isoform.ConclusionOur results provide the first survey of alternative splicing in western corn rootworm and suggest that the observed alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.

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