A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori

Chai, Chun-Li; Zhang, Ze; Huang, Feifei; Wang, Xianyan; Yu, Qiuhan; Liu, Binbin; Tian, Tian; Xia, Qingyou; Lü, Cheng; Zhang, Xiang

doi:10.1016/j.ibmb.2008.06.008

Cited by 36 publications

(47 citation statements)

References 38 publications

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“…We identified all canonical Hox genes and four copies of the special homeobox ( Shx ) genes, two ShxA , and one ShxB and C (Supplementary Figs 21 and 22; Supplementary Note 8). All the Hox genes follow the gene order and location described for other Lepidoptera, but the duplication of ShxA and lack of ShxD are distinct from other nymphalid butterflies1031.…”

Section: Resultsmentioning

confidence: 84%

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

et al. 2014

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Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n ¼ 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n ¼ 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

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Section: Resultsmentioning

confidence: 84%

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

et al. 2014

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“…It was worth mentioning that Hox genes, the well-known PcG targets in other species, were not presented in our targets analysis, except for Abdominal-B ( BmAbd-B annotated as BGIBMGA006384 in the silkworm genome). Based on the genomic information of silkworm Hox genes [28], we further checked the microarray data and found that most of the identified Hox genes were still up-regulated though with a slight change (lower than 2.0 folds and excluded in our analysis, data not shown). In addition, nine PcG targets could be mapped on the chromosome 6 (Figure 3C), where all silkworm Hox genes were also clustered [28].…”

Section: Resultsmentioning

confidence: 99%

“…Based on the genomic information of silkworm Hox genes [28], we further checked the microarray data and found that most of the identified Hox genes were still up-regulated though with a slight change (lower than 2.0 folds and excluded in our analysis, data not shown). In addition, nine PcG targets could be mapped on the chromosome 6 (Figure 3C), where all silkworm Hox genes were also clustered [28]. Thus, we speculated that PcG proteins may be recruited to this region and also involved in the regulation of the silkworm Hox genes expression.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification of Polycomb Target Genes Reveals a Functional Association of Pho with Scm in Bombyx mori

Cheng

Mon

et al. 2012

PLoS ONE

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Polycomb group (PcG) proteins are evolutionarily conserved chromatin modifiers and act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1), Polycomb repressive complex 2 (PRC2), and Pleiohomeotic repressive complex (PhoRC), to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori with holocentric centromere using genome-wide expression screening based on the knockdown of BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, the expressions of 29 genes were up-regulated after knocking down 4 PcG genes. Particularly, there is a significant overlap between targets of BmPho (331 out of 524) and BmScm (331 out of 532), and among these, 190 genes function as regulator factors playing important roles in development. We also found that BmPho, as well as BmScm, can interact with other Polycomb components examined in this study. Further detailed analysis revealed that the C-terminus of BmPho containing zinc finger domain is involved in the interaction between BmPho and BmScm. Moreover, the zinc finger domain in BmPho contributes to its inhibitory function and ectopic overexpression of BmScm is able to promote transcriptional repression by Gal4-Pho fusions including BmScm-interacting domain. Loss of BmPho expression causes relocalization of BmScm into the cytoplasm. Collectively, we provide evidence of a functional link between BmPho and BmScm, and propose two Polycomb-related repression mechanisms requiring only BmPho associated with BmScm or a whole set of PcG complexes.

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“…The following papers in this special issue cover the genomewide analyses on functions of genes controlling biological phenomena (Fujii et al, 2008;Futahashi et al, 2008;Roller et al, 2008;Katsuma et al, 2008;Chai et al, 2008;Yu et al, 2008;Duan et al, 2008;Tanaka et al, 2008), regulation of gene expression Cao et al, 2008;Kawaoka et al, 2008), specific genome structure (Osanai-Futahashi et al, 2008), and application to silkworm transgenesis (Uchino et al, 2008).…”

Section: Characteristic Biological Processesmentioning

confidence: 99%

The genome of a lepidopteran model insect, the silkworm Bombyx mori

Consortium¹

2008

Insect Biochemistry and Molecular Biology

580

258

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Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of approximately 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a GLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific tRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes.

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A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori

Cited by 36 publications

References 38 publications

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

Genome-Wide Identification of Polycomb Target Genes Reveals a Functional Association of Pho with Scm in Bombyx mori

The genome of a lepidopteran model insect, the silkworm Bombyx mori

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