Overview

Scolopendra subspinipes mutilans has been used as an herbal medicine for paralysis and arthritis in oriental medicine since ancient times, and is still widely used as an herbal medicine. About 3,000 species are distributed worldwide, and among them, the domestic centipede is known to 4 order 9 family and 44 species, but the establishment of a classification system and ecological studies are insufficient. Therefore, we intend to obtain scolopendrid's unique genes through deciphering the new genome of scolopendrid, and to provide resource data for the scientific and systematic pharmacological investigation through functional analysis of these genes.

Statistics

Genome sequencing

Scolopendrid revealed that it is composed of 28 chromosomes (2n = 28) of about 1.2 Gb of genome. A large-capacity next generation sequencing (NGS) method such as Illumina MiSeq, NextSeq sequencing and PacBio RSII sequencing, long reads sequencer, were performed for the study. As a result, a total of 525 Gb (442X) of illumina sequence (234 Gb-10 Paired-end libraries, 292 Gb-12 mate pair libraries) and 51 Gb (45X) of Pacbio reads were produced as genomic sequences.

Assembly

The scolopendrid genome consisted of a 1.1 Gb sequence consisting of the final 60,045 contigs. To this end, sequences derived from organelles such as mitochondria and genomic sequences of foreign species were removed and de novo assembly using CLC Assembly Cell was performed. N50 of the constructed genome sequence is 106,746 bp and 32.32% of GC% was confirmed. The essential gene composition ratio using CEGMA was 99.19%, which was confirmed to be very complete.

Gene prediction

In order to predict the gene, the transcript sequences of 12 tissues and developmental stages were produced, and protein sequences of 10 allied species were used. The final 21,501 genes were predicted, of which 18,219 (84.7%) were identified for biologically functioning genes. The most similar species to the scolopendrid were identified as the European land centipede (Strigamia maritima) and the velvet spider (Stegodyphus mimosarum).

Evolutionary characters

Scolopendrid is one of the largest genomes and genes among the centipedes that have already been identified, and is a representative of centipedes. In addition, the evolutionary analysis using genes across the genome revealed that it diverged about 400 million years ago from insects and about 600 million years ago from arachnids. Interestingly, many of the toxic genes found in arachnids were also found in centipedes, which can be said to be a characteristic different from insects. Among them, scolopendrasin Ⅶ, one of the toxic genes of scolopendrid, was confirmed to have good pharmacological effects in connection with autoimmune diseases in the human immune system.

Contacts

Hwang Jae Sam (email: hwangjs@korea.kr)

Lee Joon Ha (email: coover@korea.kr)

Reference Publication

Yoo WG, Lee JH, Shin Y, Shim JY, Jung M, Kang BC, Oh J, Seong J, Lee HK, Kong HS, Song KD, Yun EY, Kim IW, Kwon YN, Lee DG, Hwang UW, Park J, Hwang JS. Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans., Functional & Integrative Genomics. 2014 Jun; 14(2): 275-283.