Amynthas corticis genome reveals molecular mechanisms behind global distribution

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.

Acceleration of genome rearrangement in clitellate annelids

“…The following chromosome-scale and scaffold-level annelid and mollusk genomes, as well as their genome annotations and protein sequences, were downloaded for this project: Helobdella robusta (GCF_000326865.2) (Simakov et al 2013), Hirudinaria manillensis (GCA_034509925.1) (Guan et al 2019), Metaphire vulgaris (GCA_018105865.1) (Jin et al 2020), Amynthas corticis (GCA_900184025.1) (Wang et al 2021), Eisenia andrei (GWHACBE00000000) (Shao et al 2020), Enchytraeus crypticus (GCA_905160935.1) (Amorim et al 2021), Capitella teleta (GCA_000328365.1) (Simakov et al 2013), Streblospio benedicti (GCA_019095985.1) (Zakas et al 2022), Dimorphilus gyrociliatus (GCA_904063045.1) (Martín-Durán et al 2021), Owenia fusiformis (GCA_903813345.2) (Martín-Zamora et al 2023), Lottia gigantea (GCF_000327385.1) (Simakov et al 2013), Pecten maximus (GCA_902652985.1) (Kenny et al 2020), Riftia pachyptila (https://phaidra.univie.ac.at/detail/o:1220865) (de Oliveira et al 2022), Lepidonotus clava (GCA_936440205.1) (Darbyshire et al 2022), Sthenelais limicola (GCA_942159475.1) (Darbyshire et al 2023), Alitta virens (GCA_932294295.1) (Fletcher et al 2023), Paraescarpia echinospica (GCA_020002185.1) (Sun et al 2021), Lumbricus rubellus (GCA_945859605.1) (Short et al 2023), and Piscicola geometra (GCA_943735955.1) (Doe 2023). Additionally, we downloaded the following genomes of the simultaneously hermaphroditic species from NCBI: Biomphalaria glabrata (GCA_947242115.1) (The Darwin Tree of Life Project et al 2022), and Kryptolebias marmoratus (GCF_001649575.2).…”

“…The following chromosome-scale and scaffold-level annelid and mollusk genomes, as well as their genome annotations and protein sequences, were downloaded for this project: Helobdella robusta (GCF_000326865.2) (Simakov et al 2013), Hirudinaria manillensis (GCA_034509925.1) (Guan et al 2019), Metaphire vulgaris (GCA_018105865.1) (Jin et al 2020), Amynthas corticis (GCA_900184025.1) (Wang et al 2021), Eisenia andrei (GWHACBE00000000) (Shao et al 2020) The genomes were prepared for use with the odp software package (Schultz et al 2023) by extracting the protein coordinate information to rbh files.…”

Evolution and Function of the Notch Signaling Pathway: An Invertebrate Perspective

“…Despite studies depicting the bilobed mass brain (located above the pharynx in the third somite of earthworms), its associated sensory nerves, and other neural structures, there have been few studies on the neurodevelopmental function of Notch signaling in earthworms. Following the completion of genome assembly and analysis in the earthworm Amynthas cortici ( A. cortici ) [ 69 ], further studies can be undertaken to analyze Notch regulation in neural development or regeneration.…”

Molecular insights into high-altitude adaption and acclimatisation ofAporrectodea caliginosa

“…To investigate adaptive and acclimatised responses of earthworms to high altitude, we can look at differential expression of genes and at variation in the distribution of single-nucleotide polymorphisms (SNPs) across the genome that may be indicative of selective processes (Robledo et al, 2017). However, although such 1 analyses are readily feasible for many species that have had their genomes assembled, earthworms, as a group, are underrepresented among these with Eisenia fetida (N50 < 10 Kb), Eisenia andrei (N50 ~740 Kb), Metaphire vulgaris (N50 ~4.2 Mb), and Amynthas corticis (N50 ~31 Mb), representing the few earthworms with their genomes sequenced (Zwarycz et al, 2015;Bhambri et al, 2017 Preprint;Jin et al, 2020;Shao et al, 2020;Wang et al, 2021). Assembling a high-quality genome (N50 > 10 Kbp) for an earthworm has proved a challenge for many years because of their high allelic diversity (Rimington, 2022); however, with long-read technology combined with scaffolding techniques, it is possible to now overcome this hurdle (Ghurye & Pop, 2019).…”