A second-generation integrated map of the silkworm reveals synteny and conserved gene order between lepidopteran insects

Abstract

A second-generation linkage map was constructed for the silkworm, Bombyx mori, focusing on mapping Bombyx sequences appearing in public nucleotide databases and bacterial artificial chromosome (BAC) contigs. A total of 874 BAC contigs containing 5067 clones (22% of the library) were constructed by PCR-based screening with sequence-tagged sites (STSs) derived from whole-genome shotgun (WGS) sequences. A total of 523 BAC contigs, including 342 independent genes registered in public databases and 85 expressed sequence tags (ESTs), were placed onto the linkage map. We found significant synteny and conserved gene order between B. mori and a nymphalid butterfly, Heliconius melpomene, in four linkage groups (LGs), strongly suggesting that using B. mori as a reference for comparative genomics in Lepidotera is highly feasible.

Figure 1.—

Schematic of linkage map construction for autosomes. The linkage map shown in Figure 2 is represented by B, which is constructed from genetic distances among codominant markers (capital letters) calculated from two types of F₂ individuals (for detailed explanation, see Yasukochi 1998). A and C represent genetic distances among C108-dominant and codominant markers calculated from F₂ individuals harboring p50-derived nonrecombinant chromosomes and genetic distances among p50-dominant and codominant markers calculated from F₂ individuals harboring C108-derived nonrecombinant chromosomes, respectively. Dominant markers (small letters) located between two codominant markers were added at map positions determined by dividing the genetic distances between neighboring codominant markers in B (the integrated map) in proportion to genetic distances between the dominant marker and the neighboring codominant markers in A (C108 reference map) or in C (p50 reference map). Dominant markers located distally to codominant markers were added at genetic distances calculated between the dominant marker and the nearest codominant marker.

Figure 2.—

A linkage map for B. mori. Capital letters in parentheses indicate former designations for LGs in Yasukochi (1998). Markers listed on the left or right of the bars represent C108-dominant markers and p50-dominant markers, respectively. Codominant markers are listed on both sides of the bars. Detailed information about RAPD markers (named with the first letter R) can be obtained from Bombmap (http://sgp.dna.affrc.go.jp/bombmap/index.html).

Figure 2.—

A linkage map for B. mori. Capital letters in parentheses indicate former designations for LGs in Yasukochi (1998). Markers listed on the left or right of the bars represent C108-dominant markers and p50-dominant markers, respectively. Codominant markers are listed on both sides of the bars. Detailed information about RAPD markers (named with the first letter R) can be obtained from Bombmap (http://sgp.dna.affrc.go.jp/bombmap/index.html).

Figure 2.—

A linkage map for B. mori. Capital letters in parentheses indicate former designations for LGs in Yasukochi (1998). Markers listed on the left or right of the bars represent C108-dominant markers and p50-dominant markers, respectively. Codominant markers are listed on both sides of the bars. Detailed information about RAPD markers (named with the first letter R) can be obtained from Bombmap (http://sgp.dna.affrc.go.jp/bombmap/index.html).

Figure 2.—

A linkage map for B. mori. Capital letters in parentheses indicate former designations for LGs in Yasukochi (1998). Markers listed on the left or right of the bars represent C108-dominant markers and p50-dominant markers, respectively. Codominant markers are listed on both sides of the bars. Detailed information about RAPD markers (named with the first letter R) can be obtained from Bombmap (http://sgp.dna.affrc.go.jp/bombmap/index.html).

Figure 3.—

Correlation of genetic and physical lengths of each chromosome. The average relative size of all chromosomes is defined as 1.

Figure 4.—

Localization of genes of interest by BAC–FISH mapping. (a and b) A 6C1E BAC covering Bm-Tpi (green signal) was colocalized with three Z-BACs (9A5H, 14I7D, and 5H3E; red signals) (a) on the Z chromosome in a female mitotic complement and (b) mapped on the Z chromatid between 9A5H and 14I7D in a female pachytene complement. (c) Five independent BAC–FISH preparations with 18B2A (RpP1), 10D5C (RpP0), 15I9C (RpS8), 18D1A (Bm-opsin), 20A1F (RpS5), 8L11B (RpL5), and 10A11H (RpL7A) probes defining the representative gene order on the chromosome corresponding to LG15 (Chr 15). The yellow signal was produced with a mixture of BAC probes, 3K9A (a Chr 15 marker) labeled with Cy-3 and fluorescein. (d) The order of genes, RpL19 (9C1F), RpL13 (5D7C), Bm-EF1α(11K9B), and patched (5C10F), on the chromosome corresponding to LG5 (Chr 5) was confirmed by three BAC–FISH mapping experiments with two red-labeled BAC probes (2C2D and 7H6C).