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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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Overview of the gene-build for the silkworm genome. The white box in each gene set describes the composition of ESTs derived from FL-cDNA and cDNA libraries. ESTs used in Gene set B include ones derived from FL-cDNA libraries for which the full-length clone sequences were not yet determined.
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fig1: Overview of the gene-build for the silkworm genome. The white box in each gene set describes the composition of ESTs derived from FL-cDNA and cDNA libraries. ESTs used in Gene set B include ones derived from FL-cDNA libraries for which the full-length clone sequences were not yet determined.

Mentions: Here we report isolation and sequencing of 11,104 FL-cDNA clones chosen from 21 FL-cDNA libraries derived from 14 distinct silkworm tissues of different developmental stages. To determine a complete set of silkworm genes, we used 11,104 FL-cDNAs, 408,172 expressed sequence tags (ESTs), 2089 mRNA sequences registered in public databases, and 14,625 gene models as shown in Figure 1. We estimated the frequency of expression of a standard set of 16,823 genes, which were mapped on scaffolds and covered complete open reading frames culled from the FL-cDNA libraries and a large available EST database, and constructed a map of transcriptional expression for tissue-specific genes along the chromosomes. These data revealed distinctive patterns of tissue-specific and sexually dimorphic gene clusters. The extensive dataset we provide here should be valuable not only for studies in the silkworm but also for other insects.


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)

Overview of the gene-build for the silkworm genome. The white box in each gene set describes the composition of ESTs derived from FL-cDNA and cDNA libraries. ESTs used in Gene set B include ones derived from FL-cDNA libraries for which the full-length clone sequences were not yet determined.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3755909&req=5

fig1: Overview of the gene-build for the silkworm genome. The white box in each gene set describes the composition of ESTs derived from FL-cDNA and cDNA libraries. ESTs used in Gene set B include ones derived from FL-cDNA libraries for which the full-length clone sequences were not yet determined.
Mentions: Here we report isolation and sequencing of 11,104 FL-cDNA clones chosen from 21 FL-cDNA libraries derived from 14 distinct silkworm tissues of different developmental stages. To determine a complete set of silkworm genes, we used 11,104 FL-cDNAs, 408,172 expressed sequence tags (ESTs), 2089 mRNA sequences registered in public databases, and 14,625 gene models as shown in Figure 1. We estimated the frequency of expression of a standard set of 16,823 genes, which were mapped on scaffolds and covered complete open reading frames culled from the FL-cDNA libraries and a large available EST database, and constructed a map of transcriptional expression for tissue-specific genes along the chromosomes. These data revealed distinctive patterns of tissue-specific and sexually dimorphic gene clusters. The extensive dataset we provide here should be valuable not only for studies in the silkworm but also for other insects.

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