Abstract
BackgroundWe performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an EcoRI- and a BamHI-digested library) and conducted an in silico analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (Bombyx mori).ResultsMore than 94000 BAC end sequences (BESs), comprising more than 55 Mbp and covering about 10.4% of the silkworm genome, were sequenced. Repeat-sequence analysis with known repeat sequences indicated that the long interspersed nuclear elements (LINEs) were abundant in BamHI BESs, whereas DNA-type elements were abundant in EcoRI BESs. Repeat-sequence analysis revealed that the abundance of LINEs might be due to a GC bias of the restriction sites and that the GC content of silkworm LINEs was higher than that of mammalian LINEs. In a BLAST-based sequence analysis of the BESs against two available whole-genome shotgun sequence data sets, more than 70% of the BESs had a BLAST hit with an identity of ≥ 99%. About 14% of EcoRI BESs and about 8% of BamHI BESs were paired-end clones with unique sequences at both ends. Cluster analysis of the BESs clarified the proportion of BESs containing protein-coding regions.ConclusionAs a result of this characterization, the identified BESs will be a valuable resource for genomic research on Bombyx mori, for example, as a base for construction of a BAC-based physical map. The use of multiple complementary BAC libraries constructed with different restriction enzymes also makes the BESs a more valuable genomic resource. The GenBank accession numbers of the obtained end sequences are DE283657–DE378560.
Highlights
We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two Bacterial artificial chromosomes (BACs) libraries and conducted an in silico analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (Bombyx mori)
The GC bias of BamHI may be main factor accounting for this difference because the GC% of BamHI recognition sites was relatively close to the estimated GC% of protein coding DNA of the silkworm genome
These results indicate that the use of multiple BAC libraries constructed with different restriction enzymes can increase the genome representation [39]
Summary
We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an EcoRI- and a BamHI-digested library) and conducted an in silico analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (Bombyx mori). Besides being used for silk production, the silkworm is an effective host for the production of recombinant proteins and biomaterials [13]. It is an important model organism of the Lepidoptera, the insect order that includes the majority of serious agricultural pests. BMC Genomics 2007, 8:314 http://www.biomedcentral.com/1471-2164/8/314 trol of agricultural pests and the development of the silkworm as an industrial-scale resource of biomaterials or bioreactors. BACs are one of the main tools used for high-throughput genomic studies, including for sequence-tagged connector (STC) strategies, BAC-based physical maps, and DNA fingerprinting, in various species [12,13,14,15,16,17,18,19,20,21,22,23,24,25,26]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
