Abstract
Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.
Highlights
Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries
To evaluate the ploidy of the genome of A. corticis, we called genome-wide SNPs and constructed the coverage distribution of heterozygous k-mer based on resequencing data of A. corticis individuals
The result of statistical analysis based on the density distribution of allele frequency related to SNPs on biallelic loci shows that the triploid hypothesis possesses the lowest delta log-likelihood[31,32] (Fig. 2b), suggesting the genome of A. corticis is most probably triploid
Summary
Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability. To reveal the whole picture of molecular mechanisms behind the ecological plasticity and adaptation of A. corticis, we sequenced its genome and generated a complete 1.2 Gb assembly[16], including 42 chromosome-level scaffolds with N50 length of 31 Mb (Table 1 and Supplementary Fig. 3) and annotated a total of 29,256 protein-coding genes in the genome (Supplementary data file 1). In addition to the genome, we performed iTRAQ-based quantitative proteomics analysis to detect differentially expressed proteins of A. corticis and sequenced 16 S rDNA from its intestinal tract after treatment
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