High-quality genome assembly of the silkworm, Bombyx mori

Kawamoto, Munetaka; Jouraku, Akiya; Toyoda, Atsushi; Yokoi, Kakeru; Minakuchi, Yohei; Katsuma, Susumu; Fujiyama, Asao; Kiuchi, Takashi; Yamamoto, Kimiko; Shimada, Toru

doi:10.1016/j.ibmb.2019.02.002

Cited by 235 publications

(300 citation statements)

References 45 publications

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“…We annotated protein-coding genes using three approaches: homology-based, transcript-based, and de novo gene prediction. We used protein sets from Papilio machaon (21), Pieris rapae (9), Calycopis cecrops (10), Calephelis nemesis (8), Danaus plexippus (4), Cecropterus lyciades (7), Bombyx mori (87), and Drosophila melanogaster (88) as references for homology-based annotation. These references include one species from each of the 6 butterfly families and the established model organisms, silkworm and fruit fly with expected high quality of gene models.…”

Section: Reference Genome Assembly and Annotationmentioning

confidence: 99%

Genomics of a complete butterfly continent

Zhang

Cong

Shen

et al. 2019

Preprint

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Never before have we had the luxury of choosing a continent, picking a large phylogenetic group of animals, and obtaining genomic data for its every species. Here, we sequence all 845 species of butterflies recorded from North America north of Mexico. Our comprehensive approach reveals the pattern of diversification and adaptation occurring in this phylogenetic lineage as it has spread over the continent, which cannot be seen on a sample of selected species. We observe bursts of diversification that generated taxonomic ranks: subfamily, tribe, subtribe, genus, and species. The older burst around 70 Mya resulted in the butterfly subfamilies, with the major evolutionary inventions being unique phenotypic traits shaped by high positive selection and gene duplications. The recent burst around 5 Mya is caused by explosive radiation in diverse butterfly groups associated with diversification in transcription and mRNA regulation, morphogenesis, and mate selection. Rapid radiation correlates with more frequent introgression of speciation-promoting and beneficial genes among radiating species. Radiation and extinction patterns over the last 100 million years suggest the following general model of animal evolution. A population spreads over the land, adapts to various conditions through mutations, and diversifies into several species. Occasional hybridization between these species results in accumulation of beneficial alleles in one, which eventually survives, while others become extinct. Not only butterflies, but also the hominids may have followed this path.Butterflies are among the most beloved animals , beautiful and harmless, they have attracted human attention since prehistoric times (1). Being one of the best-studied insects phenotypically (2), butterflies remain largely unexplored by genomics. Until recently, genomic studies of butterflies were confined to a couple of model organisms and pests, such as Heliconius, monarch, and cabbage white, with initial studies leading to groundbreaking insights into mimicry, migration, and toxin resistance (3-5). We have been expanding these efforts on butterfly genomics to cover a broader range of species (6-11). With the rapid decrease in the price of DNA sequencing and the constant development of analytical methods, the time is ripe to sequence the genomes of all butterfly species over a continent.

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Section: Reference Genome Assembly and Annotationmentioning

confidence: 99%

Genomics of a complete butterfly continent

Zhang

Cong

Shen

et al. 2019

Preprint

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“…The trio binned A. plantaginis assemblies are of comparable quality to the best reference genomes available for Lepidoptera (Table 2; Figure 3B). When compared to other published lepidopteran reference genomes, quality of the A. plantaginis assemblies surpasses all but the best Heliconius melpomene [32] and Bombyx mori [35] assemblies (Table 2; Figure 3B). As contiguity of the H. melpomene assembly was improved through pedigree linkage mapping and haplotypic sequence merging [32], whilst bacterial artificial chromosome (BAC) and…”

Section: Quality Assessmentmentioning

confidence: 95%

“…Quality comparisons were conducted against an assembly of unbinned data from the same F1 offspring (iArcPla.wtdbg2), and against a representative selection of published lepidopteran reference genomes. For this, the latest versions of seven Lepidoptera species were downloaded: Bicyclus anynana version 1.2 [30], Danaus plexippus version 3 [31], Heliconius melpomene version Hmel.2.5 [32], Manduca sexta version Msex_1.0 [33] and Melitaea cinxia version MelCinx1.0 [34] were downloaded from Lepbase version 4.0 [11], whilst Bombyx mori version Bomo_genome_assembly [35] was downloaded from SilkBase version 2.1 [36] and Trichoplusia ni version PPHH01.1 [37] was downloaded from NCBI RefSeq version 94 [38]. Cumulative scaffold plots were visualised in R version 3.5.1 [39] using the ggplot2 package version 3.1.1 [40].…”

Section: Quality Assessmentmentioning

confidence: 99%

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A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

Yen

McCarthy

Galarza

et al. 2020

Preprint

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Background: Diploid genome assembly is typically impeded by heterozygosity, as it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution which exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. Findings: We produced a highquality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ~1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked-reads. Both assemblies are highly contiguous (mean scaffold N50: 8.2Mb) and complete (mean BUSCO completeness: 97.3%), with complete annotations and 31 chromosomes identified through karyotyping. We employed the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from five populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. Conclusions:We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling highly heterozygous genomes. Using this assembly, we provide genomic insights into geographic population structure of Arctia plantaginis.

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“…Reference transcriptome data using this genome sequence and the predicted gene set and transcriptome profile of important tissues significantly contribute to advances in silkworm and Lepidopteran research. In the present study, we constructed a reference transcript sequence data set using the RNA-seq data of 10 important tissues from silkworm larvae and reference genome data for improving the predicted gene set data of Kawamoto et al (2019) (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

Reference transcriptome data in silkwormBombyx mori

Yokoi

Tsubota

Sun

et al. 2019

Preprint

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The silkworm Bombyx mori has long been used in the silk industry and utilized in studies of physiology, genetics, molecular biology, and pathology. We recently reported high quality reference genome data for B. mori. In the present study, we constructed a reference transcriptome data set using the reference genome data and RNA-seq data of 10 tissues from P50T strain larvae. Reference transcriptome data contained 51,926 transcripts, with 39,619 having one or more coding sequence region. The abundance of each transcript in the 10 tissues as well as 5 tissues from other strain larvae was estimated, and hierarchical clustering was performed. The results obtained showed that data on abundance were highly reproducible and there here is a little difference of transcriptome abundance between the two strain larvae. New isoforms of silk-related genes were searched for in the reference transcriptomes, and the longest isoform of sericin-1 possessing a long exon was identified. We also extracted transcripts that were strongly expressed in one or more parts of the silk glands. An enrichment analysis performed using the functional annotation data of the transcripts provided novel insights into the functions of the silk gland parts. Therefore, the reference transcriptome data set obtained has extended B. mori genomic and transcriptomic insights and may contribute to advances in entomologic and vertebrate research, including that on humans.

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High-quality genome assembly of the silkworm, Bombyx mori

Cited by 235 publications

References 45 publications

Genomics of a complete butterfly continent

Genomics of a complete butterfly continent

A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

Reference transcriptome data in silkwormBombyx mori

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