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Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.

Suetsugu Y, Futahashi R, Kanamori H, Kadono-Okuda K, Sasanuma S, Narukawa J, Ajimura M, Jouraku A, Namiki N, Shimomura M, Sezutsu H, Osanai-Futahashi M, Suzuki MG, Daimon T, Shinoda T, Taniai K, Asaoka K, Niwa R, Kawaoka S, Katsuma S, Tamura T, Noda H, Kasahara M, Sugano S, Suzuki Y, Fujiwara H, Kataoka H, Arunkumar KP, Tomar A, Nagaraju J, Goldsmith MR, Feng Q, Xia Q, Yamamoto K, Shimada T, Mita K - G3 (Bethesda) (2013)

Bottom Line: The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics.More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters.The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences, Tsukuba 305-8634, Japan.

ABSTRACT
The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics. A more complete annotation of the genome will benefit functional and comparative studies and accelerate extensive industrial applications for this insect. To realize these goals, we embarked upon a large-scale full-length cDNA collection from 21 full-length cDNA libraries derived from 14 tissues of the domesticated silkworm and performed full sequencing by primer walking for 11,104 full-length cDNAs. The large average intron size was 1904 bp, resulting from a high accumulation of transposons. Using gene models predicted by GLEAN and published mRNAs, we identified 16,823 gene loci on the silkworm genome assembly. Orthology analysis of 153 species, including 11 insects, revealed that among three Lepidoptera including Monarch and Heliconius butterflies, the 403 largest silkworm-specific genes were composed mainly of protective immunity, hormone-related, and characteristic structural proteins. Analysis of testis-/ovary-specific genes revealed distinctive features of sexual dimorphism, including depletion of ovary-specific genes on the Z chromosome in contrast to an enrichment of testis-specific genes. More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters. The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes.

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Map of thirty-three 30-kDa protein genes forming a cluster on chromosome 20. In the first gene cluster composed of nineteen 30-kDa protein genes, four fat body-specific genes and one MT-specific 30kDa protein gene (red) are located in the former half of the cluster, whereas nine 30-kDa protein genes mainly expressed in brain-nervous system (blue) occupy the latter half of the cluster. Six genes showed no hit in the EST database (gray). A second 30-kDa protein gene cluster composed of 14 genes was located 440 kb from the former gene cluster. Nine of fourteen genes were specifically expressed in an embryonic stage (green), whereas one was mainly expressed in fat body; the remaining four genes showed no hit in the EST db.
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fig6: Map of thirty-three 30-kDa protein genes forming a cluster on chromosome 20. In the first gene cluster composed of nineteen 30-kDa protein genes, four fat body-specific genes and one MT-specific 30kDa protein gene (red) are located in the former half of the cluster, whereas nine 30-kDa protein genes mainly expressed in brain-nervous system (blue) occupy the latter half of the cluster. Six genes showed no hit in the EST database (gray). A second 30-kDa protein gene cluster composed of 14 genes was located 440 kb from the former gene cluster. Nine of fourteen genes were specifically expressed in an embryonic stage (green), whereas one was mainly expressed in fat body; the remaining four genes showed no hit in the EST db.

Mentions: Biosynthesis of the Lepidoptera-specific 30-kDa lipoprotein gene family whose function is not fully understood occurs in a stage-dependent fashion in fat body (Ujita et al. 2002). We found thirty-three 30-kD a protein genes localized in an 820-kb region of ch.20 forming two gene clusters (Figure 6, Table S5). The first gene cluster in the region spanning 3,412,956−3,565,568 harbored nineteen 30-kDa protein genes; four of these were fat body-specific and one was malpighian tubule (MT)-specific. Interestingly, whereas three of the 19 genes in the cluster seemed not to express, nine genes were transcribed extensively and primarily in the brain-nervous system. The expression levels of these nine genes were significantly greater than in fat body (Table S5), indicating the brain-nervous system is a major contributor of 30-kDa protein transcripts. In addition, the four fat body and MT-specific genes were localized in the 5′ portion of the gene cluster, whereas the nine genes expressed mainly in brain-nervous system occupied the other half of the cluster (Figure 6). The second gene cluster spanning the region 4,012,903−4,227,867 was composed of fourteen 30-kDa protein genes, nine of which expressed exclusively or mainly at an embryonic stage (Figure 6; Table S5). These observations suggest an as yet-unknown function for 30-kDa proteins that has not been reported previously and further support the idea of tissue-specific chromosome domains.


Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.

Suetsugu Y, Futahashi R, Kanamori H, Kadono-Okuda K, Sasanuma S, Narukawa J, Ajimura M, Jouraku A, Namiki N, Shimomura M, Sezutsu H, Osanai-Futahashi M, Suzuki MG, Daimon T, Shinoda T, Taniai K, Asaoka K, Niwa R, Kawaoka S, Katsuma S, Tamura T, Noda H, Kasahara M, Sugano S, Suzuki Y, Fujiwara H, Kataoka H, Arunkumar KP, Tomar A, Nagaraju J, Goldsmith MR, Feng Q, Xia Q, Yamamoto K, Shimada T, Mita K - G3 (Bethesda) (2013)

Map of thirty-three 30-kDa protein genes forming a cluster on chromosome 20. In the first gene cluster composed of nineteen 30-kDa protein genes, four fat body-specific genes and one MT-specific 30kDa protein gene (red) are located in the former half of the cluster, whereas nine 30-kDa protein genes mainly expressed in brain-nervous system (blue) occupy the latter half of the cluster. Six genes showed no hit in the EST database (gray). A second 30-kDa protein gene cluster composed of 14 genes was located 440 kb from the former gene cluster. Nine of fourteen genes were specifically expressed in an embryonic stage (green), whereas one was mainly expressed in fat body; the remaining four genes showed no hit in the EST db.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3755909&req=5

fig6: Map of thirty-three 30-kDa protein genes forming a cluster on chromosome 20. In the first gene cluster composed of nineteen 30-kDa protein genes, four fat body-specific genes and one MT-specific 30kDa protein gene (red) are located in the former half of the cluster, whereas nine 30-kDa protein genes mainly expressed in brain-nervous system (blue) occupy the latter half of the cluster. Six genes showed no hit in the EST database (gray). A second 30-kDa protein gene cluster composed of 14 genes was located 440 kb from the former gene cluster. Nine of fourteen genes were specifically expressed in an embryonic stage (green), whereas one was mainly expressed in fat body; the remaining four genes showed no hit in the EST db.
Mentions: Biosynthesis of the Lepidoptera-specific 30-kDa lipoprotein gene family whose function is not fully understood occurs in a stage-dependent fashion in fat body (Ujita et al. 2002). We found thirty-three 30-kD a protein genes localized in an 820-kb region of ch.20 forming two gene clusters (Figure 6, Table S5). The first gene cluster in the region spanning 3,412,956−3,565,568 harbored nineteen 30-kDa protein genes; four of these were fat body-specific and one was malpighian tubule (MT)-specific. Interestingly, whereas three of the 19 genes in the cluster seemed not to express, nine genes were transcribed extensively and primarily in the brain-nervous system. The expression levels of these nine genes were significantly greater than in fat body (Table S5), indicating the brain-nervous system is a major contributor of 30-kDa protein transcripts. In addition, the four fat body and MT-specific genes were localized in the 5′ portion of the gene cluster, whereas the nine genes expressed mainly in brain-nervous system occupied the other half of the cluster (Figure 6). The second gene cluster spanning the region 4,012,903−4,227,867 was composed of fourteen 30-kDa protein genes, nine of which expressed exclusively or mainly at an embryonic stage (Figure 6; Table S5). These observations suggest an as yet-unknown function for 30-kDa proteins that has not been reported previously and further support the idea of tissue-specific chromosome domains.

Bottom Line: The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics.More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters.The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences, Tsukuba 305-8634, Japan.

ABSTRACT
The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics. A more complete annotation of the genome will benefit functional and comparative studies and accelerate extensive industrial applications for this insect. To realize these goals, we embarked upon a large-scale full-length cDNA collection from 21 full-length cDNA libraries derived from 14 tissues of the domesticated silkworm and performed full sequencing by primer walking for 11,104 full-length cDNAs. The large average intron size was 1904 bp, resulting from a high accumulation of transposons. Using gene models predicted by GLEAN and published mRNAs, we identified 16,823 gene loci on the silkworm genome assembly. Orthology analysis of 153 species, including 11 insects, revealed that among three Lepidoptera including Monarch and Heliconius butterflies, the 403 largest silkworm-specific genes were composed mainly of protective immunity, hormone-related, and characteristic structural proteins. Analysis of testis-/ovary-specific genes revealed distinctive features of sexual dimorphism, including depletion of ovary-specific genes on the Z chromosome in contrast to an enrichment of testis-specific genes. More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters. The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes.

Show MeSH
Related in: MedlinePlus