End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome libraries
<p>Abstract</p> <p>Background</p> <p>We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an <it>Eco</it>RI- and a <it>Bam</it>HI-digested library) and conducted an <it>in silico </it>ana...
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doaj-99d3a6f444b2450d8eb8ba5e0a9bf3b12020-11-25T01:03:38ZengBMCBMC Genomics1471-21642007-09-018131410.1186/1471-2164-8-314End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome librariesNarukawa JunkoSasanuma Shun-ichiShimomura MichihikoMinami HiroshiSuetsugu YoshitakaMita KazueiYamamoto Kimiko<p>Abstract</p> <p>Background</p> <p>We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an <it>Eco</it>RI- and a <it>Bam</it>HI-digested library) and conducted an <it>in silico </it>analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (<it>Bombyx mori</it>).</p> <p>Results</p> <p>More 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 <it>Bam</it>HI BESs, whereas DNA-type elements were abundant in <it>Eco</it>RI 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 <it>Eco</it>RI BESs and about 8% of <it>Bam</it>HI 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.</p> <p>Conclusion</p> <p>As a result of this characterization, the identified BESs will be a valuable resource for genomic research on <it>Bombyx mori</it>, 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 <ext-link ext-link-type="gen" ext-link-id="DE283657">DE283657</ext-link>–<ext-link ext-link-type="gen" ext-link-id="DE378560">DE378560</ext-link>.</p> http://www.biomedcentral.com/1471-2164/8/314 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Narukawa Junko Sasanuma Shun-ichi Shimomura Michihiko Minami Hiroshi Suetsugu Yoshitaka Mita Kazuei Yamamoto Kimiko |
spellingShingle |
Narukawa Junko Sasanuma Shun-ichi Shimomura Michihiko Minami Hiroshi Suetsugu Yoshitaka Mita Kazuei Yamamoto Kimiko End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome libraries BMC Genomics |
author_facet |
Narukawa Junko Sasanuma Shun-ichi Shimomura Michihiko Minami Hiroshi Suetsugu Yoshitaka Mita Kazuei Yamamoto Kimiko |
author_sort |
Narukawa Junko |
title |
End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome libraries |
title_short |
End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome libraries |
title_full |
End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome libraries |
title_fullStr |
End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome libraries |
title_full_unstemmed |
End-sequencing and characterization of silkworm (<it>Bombyx mori</it>) bacterial artificial chromosome libraries |
title_sort |
end-sequencing and characterization of silkworm (<it>bombyx mori</it>) bacterial artificial chromosome libraries |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2007-09-01 |
description |
<p>Abstract</p> <p>Background</p> <p>We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an <it>Eco</it>RI- and a <it>Bam</it>HI-digested library) and conducted an <it>in silico </it>analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (<it>Bombyx mori</it>).</p> <p>Results</p> <p>More 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 <it>Bam</it>HI BESs, whereas DNA-type elements were abundant in <it>Eco</it>RI 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 <it>Eco</it>RI BESs and about 8% of <it>Bam</it>HI 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.</p> <p>Conclusion</p> <p>As a result of this characterization, the identified BESs will be a valuable resource for genomic research on <it>Bombyx mori</it>, 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 <ext-link ext-link-type="gen" ext-link-id="DE283657">DE283657</ext-link>–<ext-link ext-link-type="gen" ext-link-id="DE378560">DE378560</ext-link>.</p> |
url |
http://www.biomedcentral.com/1471-2164/8/314 |
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