ABSTRACT
The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.
Subject(s)
Bombyx , Genome, Insect , Animals , Bombyx/genetics , Computational Biology , Genomics , Metadata , MultiomicsABSTRACT
The spread of COVID-19 results in a significant drop in traffic levels worldwide. Quantifying the impact of multiple COVID-19 outbreaks on traffic systems is critical to developing differentiated policies in the future. This paper proposes a novel COVID-19 multiple outbreak analysis method (NCMOA), dividing the impact scope and degree under multiple COVID-19 disturbances, and using the recovery rate and accumulated loss to quantify the impacts on air passenger flow. A case study based on Chinese national air traffic flow is executed, and the recovery patterns and the differentiated disturbances are analyzed. Results show that air passenger flow recovers with a similar pattern after the first outbreak, and subsequent outbreaks cause local effects and cannot affect the overall recovery pattern. Further, the heterogeneous influence factors and trends on the epi-centers (EC) and the nation are analyzed. In addition, the methods and results of this paper quantify the impact of COVID-19 on air passenger flow at a more detailed level under multiple disturbances. They could provide a basis for differentiated policy formulation of airlines and government in the future.
ABSTRACT
The silkworm Bombyx mori is an important economic insect for producing silk, the "queen of fabrics". The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.
