Moreover, swallowtail butterflies are one of the most widely studied groups of insects and are considered model organisms in a number of fields, including genetics, ecology, evolutionary biology, conservation biology, development, etc. , Papilionidae was phylogenetically placed at the basal position as a sister group to all remaining butterflies. Owing to the colorful wing color patterns and the extensive morphological diversity among the species, sexes, populations, and seasonal forms, it is widely regarded as one of the most popular and esthetically attractive butterflies and of great significance for exploring the morphological diversification and speciation of butterflies. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.Īmong the 18,000+ known butterfly species (Lepidoptera: Papilionoidea), the family Papilionidae Latreille 1802, commonly known as swallowtail butterflies, comprises more than 3% of all butterfly species. Additionally, strong synteny exists between the chromosomes of P. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% ( n = 1367) BUSCO completeness. elwesi using the PacBio and PromethION platforms, respectively. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. Therefore, many assemblies stay indefinitely as collections of contigs and/or scaffolds regardless of the organism's genomic complexity.A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. Note that researchers may halt their sequencing/assembling efforts once they gather the information they need. While it is possible to generate complete assemblies for prokaryotes - where genomes are single circular chromosomes - and lower eukaryotes (such as yeast), this level is currently unattainable for the complex genomes of higher eukaryotes (including human). Finally, a non-nuclear genome (such as mitochondrion) may complete the collection for the assembly.Ĭomplete assemblies will have no sequencing gaps in the assembled chromosomes. In addition to the primary assembly, a genome assembly may contain other sequence records, such as patches (to correct regions of the primary assembly) and/or alternative loci (to offer alternative models for highly variable regions of chromosomes). Unlocalized* and unplaced** contigs and scaffolds records may accompany the chromosome records and together constitute the primary assembly. An assembly at the chromosome level will generally have one record for each chromosome. Again, researchers represent any sequencing gaps in an assembled chromosome with NNN's. ![]() The next step is to have the scaffolds that belong to the same chromosome properly ordered, oriented, and assembled into the chromosome sequence. Assemblies at the scaffold level will generally have a number of scaffold records plus a number of contigs records. To make a scaffold a single sequence unit (a single sequence record), they represent sequencing gaps between the contigs in the scaffold with series of NNN’s (instead of DNA sequence of A, T, G, and C). To build a scaffold, researchers place several contigs in the correct order and orientation. The next step is to build scaffolds (supercontigs). This approach is termed Whole Genome Shotgun ( WGS) sequencing.Ĭontigs are the first level in the hierarchy of a genomic assembly. Once the sequences of the small pieces - called reads - are obtained, researchers assemble these like tiny pieces of a giant puzzle into progressively larger contiguous sequence pieces (called contigs). A major strategy to generate an assembly involves (1) isolation of genomic DNA from a biological sample and (2) fragmentation of DNA into small pieces that are then sequenced individually.
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