About Bean Beetle Genome Sequence

The sequence data are for a laboratory strain of Callosobruchus maculatus that as been reared on mung beans (Vigna radiata) for more than 20 years (more than 200 generations). We created inbred lines by carrying out full-sib matings for 5 generations. We pooled beetles from several full-sib families with the same grandparents for sequencing. Genomic DNA was extracted from 50 females from 3 families and 70 males from 6 families, using a modified Qiagen protocol for insect DNA. The sequencing was done in a single lane of an Illumina sequencer. For more details on Illumina sequencing, see the Next Generation Sequencing Tour on the Genomics Education Partnership website (http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/nextgen_video_tour). The initial de novo assemblies were created for both male and female sequence data using CLC Genomics Workbench. The more recent de novo assembly was created for the combined male and female sequence data using Newbler and SOAP.

Basic stats about the sequence

The initial de novo assemblies contain 369,385 and 388,839 contigs for females and males, respectively. The average contig lengths are less than 500 BP. The GC content for both males and females was 37%. The more recent assembly has 85859 scaffolds. Scaffolds range from 2000 bp to 38.27 Kb. The N50 is 3818 bp. The total length of scaffolds is 315 Mb out of an estimated 1301 Mb. Although this represents about 25% coverage, greater than 50% of available ESTs map to the assembly. The GC content is 34%.

Acknowledgements

The bean beetle sequencing project was funded by a supplement to a National Science Foundation grant to Dr. Christopher Beck (Emory University) and Dr. Lawrence Blumer (Morehouse College) to develop bean beetles for inquiry-based teaching in laboratory courses (DUE-0815135, and DUE-0814373). Dr. Nicole Gerardo in the Department of Biology at Emory University provided expert advice throughout the project, and Stephanie Chiang carried out the DNA extraction in the Gerardo lab. The sequencing was done by the Emory GRA Genome Center under the direction of Dr. Tim Read and supported by the Georgia Research Alliance (GRA), the Atlanta Clinical & Translational Science Institute (ACTSI) and the Emory University Department of Human Genetics. Dr. Karla Passalaqua in the Department of Biology at Emory University produced the initial genome assemblies. Tom de Man, a visiting researcher, in the Gerardo lab in the Department of Biology at Emory University produced the more recent genome assembly.