BAC library construction and BAC end sequencing of five Drosophila species

The comparative map with the D. melanogaster genome

Katsuhiko Murakami, Atsushi Toyoda, Masahira Hattori, Yoko Kuroki, Asao Fujiyama, Toshio Kojima, Muneo Matsuda, Yoshiyuki Sakaki, Masa Toshi Yamamoto

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

We constructed and characterized arrayed bacterial artificial chromosome (BAC) libraries of five Drosophila species (D. melanogaster, D. simulans, D. sechellia, D. auraria, and D. ananassae), which are genetically well characterized in the studies of meiosis, evolution, population genetics, and developmental biology. The BAC libraries comprise 8,000 to 12,500 clones for each species, estimated to cover the most of the genomes. We sequenced both ends of most of these BAC clones with a success rate of 91%. Of these, 53,701 clones consisting of non-repetitive BAC end sequences (BESs) were mapped with reference of the public D. melanogaster genome sequences. The BES mapping estimated that the BAC libraries of D. auraria and D. ananassae covered 47% and 57% of the D. melanogaster genome, respectively, and those of D. melanogaster, D. sechellia, and D. simulans covered 94-97%. The low coverage by BESs of D. auraria and D. ananassae may be due to the high sequence divergence with D. melanogaster. From the comparative BES mapping, 111 possible breakpoints of chromosomal rearrangements were identified in these four species. The breakpoints of the major chromosome rearrangement between D. simulans and D. melanogaster on the third chromosome were determined within 20 kb in 84E and 30 kb in 93E/F. Corresponding breakpoints were also identified in D. sechellia. The BAC clones described here will be an important addition to the Drosophila genomic resources.

Original languageEnglish
Pages (from-to)245-256
Number of pages12
JournalGenes and Genetic Systems
Volume83
Issue number3
DOIs
Publication statusPublished - 2008
Externally publishedYes

Fingerprint

Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Chromosomes
Melanogaster
Drosophila
Drosophila melanogaster
Genes
Genome
genome
Clone Cells
clones
Drosophila sechellia
Chromosomes, Human, 13-15
Chromosome Breakpoints
chromosomes
Developmental Biology
Drosophila simulans
Meiosis
Population Genetics
meiosis

Keywords

  • BAC end sequence (BES)
  • BAC library
  • Chromosomal rearrangement
  • Drosophila
  • Genome evolution

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Genetics
  • Genetics(clinical)

Cite this

BAC library construction and BAC end sequencing of five Drosophila species : The comparative map with the D. melanogaster genome. / Murakami, Katsuhiko; Toyoda, Atsushi; Hattori, Masahira; Kuroki, Yoko; Fujiyama, Asao; Kojima, Toshio; Matsuda, Muneo; Sakaki, Yoshiyuki; Yamamoto, Masa Toshi.

In: Genes and Genetic Systems, Vol. 83, No. 3, 2008, p. 245-256.

Research output: Contribution to journalArticle

Murakami, K, Toyoda, A, Hattori, M, Kuroki, Y, Fujiyama, A, Kojima, T, Matsuda, M, Sakaki, Y & Yamamoto, MT 2008, 'BAC library construction and BAC end sequencing of five Drosophila species: The comparative map with the D. melanogaster genome', Genes and Genetic Systems, vol. 83, no. 3, pp. 245-256. https://doi.org/10.1266/ggs.83.245
Murakami, Katsuhiko ; Toyoda, Atsushi ; Hattori, Masahira ; Kuroki, Yoko ; Fujiyama, Asao ; Kojima, Toshio ; Matsuda, Muneo ; Sakaki, Yoshiyuki ; Yamamoto, Masa Toshi. / BAC library construction and BAC end sequencing of five Drosophila species : The comparative map with the D. melanogaster genome. In: Genes and Genetic Systems. 2008 ; Vol. 83, No. 3. pp. 245-256.
@article{8d201c399e094d9585ede0912ad74b05,
title = "BAC library construction and BAC end sequencing of five Drosophila species: The comparative map with the D. melanogaster genome",
abstract = "We constructed and characterized arrayed bacterial artificial chromosome (BAC) libraries of five Drosophila species (D. melanogaster, D. simulans, D. sechellia, D. auraria, and D. ananassae), which are genetically well characterized in the studies of meiosis, evolution, population genetics, and developmental biology. The BAC libraries comprise 8,000 to 12,500 clones for each species, estimated to cover the most of the genomes. We sequenced both ends of most of these BAC clones with a success rate of 91{\%}. Of these, 53,701 clones consisting of non-repetitive BAC end sequences (BESs) were mapped with reference of the public D. melanogaster genome sequences. The BES mapping estimated that the BAC libraries of D. auraria and D. ananassae covered 47{\%} and 57{\%} of the D. melanogaster genome, respectively, and those of D. melanogaster, D. sechellia, and D. simulans covered 94-97{\%}. The low coverage by BESs of D. auraria and D. ananassae may be due to the high sequence divergence with D. melanogaster. From the comparative BES mapping, 111 possible breakpoints of chromosomal rearrangements were identified in these four species. The breakpoints of the major chromosome rearrangement between D. simulans and D. melanogaster on the third chromosome were determined within 20 kb in 84E and 30 kb in 93E/F. Corresponding breakpoints were also identified in D. sechellia. The BAC clones described here will be an important addition to the Drosophila genomic resources.",
keywords = "BAC end sequence (BES), BAC library, Chromosomal rearrangement, Drosophila, Genome evolution",
author = "Katsuhiko Murakami and Atsushi Toyoda and Masahira Hattori and Yoko Kuroki and Asao Fujiyama and Toshio Kojima and Muneo Matsuda and Yoshiyuki Sakaki and Yamamoto, {Masa Toshi}",
year = "2008",
doi = "10.1266/ggs.83.245",
language = "English",
volume = "83",
pages = "245--256",
journal = "Genes and Genetic Systems",
issn = "1341-7568",
publisher = "Genetics Society of Japan",
number = "3",

}

TY - JOUR

T1 - BAC library construction and BAC end sequencing of five Drosophila species

T2 - The comparative map with the D. melanogaster genome

AU - Murakami, Katsuhiko

AU - Toyoda, Atsushi

AU - Hattori, Masahira

AU - Kuroki, Yoko

AU - Fujiyama, Asao

AU - Kojima, Toshio

AU - Matsuda, Muneo

AU - Sakaki, Yoshiyuki

AU - Yamamoto, Masa Toshi

PY - 2008

Y1 - 2008

N2 - We constructed and characterized arrayed bacterial artificial chromosome (BAC) libraries of five Drosophila species (D. melanogaster, D. simulans, D. sechellia, D. auraria, and D. ananassae), which are genetically well characterized in the studies of meiosis, evolution, population genetics, and developmental biology. The BAC libraries comprise 8,000 to 12,500 clones for each species, estimated to cover the most of the genomes. We sequenced both ends of most of these BAC clones with a success rate of 91%. Of these, 53,701 clones consisting of non-repetitive BAC end sequences (BESs) were mapped with reference of the public D. melanogaster genome sequences. The BES mapping estimated that the BAC libraries of D. auraria and D. ananassae covered 47% and 57% of the D. melanogaster genome, respectively, and those of D. melanogaster, D. sechellia, and D. simulans covered 94-97%. The low coverage by BESs of D. auraria and D. ananassae may be due to the high sequence divergence with D. melanogaster. From the comparative BES mapping, 111 possible breakpoints of chromosomal rearrangements were identified in these four species. The breakpoints of the major chromosome rearrangement between D. simulans and D. melanogaster on the third chromosome were determined within 20 kb in 84E and 30 kb in 93E/F. Corresponding breakpoints were also identified in D. sechellia. The BAC clones described here will be an important addition to the Drosophila genomic resources.

AB - We constructed and characterized arrayed bacterial artificial chromosome (BAC) libraries of five Drosophila species (D. melanogaster, D. simulans, D. sechellia, D. auraria, and D. ananassae), which are genetically well characterized in the studies of meiosis, evolution, population genetics, and developmental biology. The BAC libraries comprise 8,000 to 12,500 clones for each species, estimated to cover the most of the genomes. We sequenced both ends of most of these BAC clones with a success rate of 91%. Of these, 53,701 clones consisting of non-repetitive BAC end sequences (BESs) were mapped with reference of the public D. melanogaster genome sequences. The BES mapping estimated that the BAC libraries of D. auraria and D. ananassae covered 47% and 57% of the D. melanogaster genome, respectively, and those of D. melanogaster, D. sechellia, and D. simulans covered 94-97%. The low coverage by BESs of D. auraria and D. ananassae may be due to the high sequence divergence with D. melanogaster. From the comparative BES mapping, 111 possible breakpoints of chromosomal rearrangements were identified in these four species. The breakpoints of the major chromosome rearrangement between D. simulans and D. melanogaster on the third chromosome were determined within 20 kb in 84E and 30 kb in 93E/F. Corresponding breakpoints were also identified in D. sechellia. The BAC clones described here will be an important addition to the Drosophila genomic resources.

KW - BAC end sequence (BES)

KW - BAC library

KW - Chromosomal rearrangement

KW - Drosophila

KW - Genome evolution

UR - http://www.scopus.com/inward/record.url?scp=48949105039&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=48949105039&partnerID=8YFLogxK

U2 - 10.1266/ggs.83.245

DO - 10.1266/ggs.83.245

M3 - Article

VL - 83

SP - 245

EP - 256

JO - Genes and Genetic Systems

JF - Genes and Genetic Systems

SN - 1341-7568

IS - 3

ER -