Phillips, H. R. P. et al. Global distribution of earthworm diversity. Science 366, 480–485 (2019).
Darwin, C. The Formation of Vegetable Mould Through the Action of Worms. (Cambridge Univ. Press, 1881).
Vila, M. B. C. & Pysek, P. How well do we understand the impacts of alien species on ecosystem services? A pan‐European, cross‐taxa assessment. Front. Ecol. Environ. 8, 135–144 (2010).
Callaham, M. A. Pandora’s box contained bait: the global problem of introduced earthworms. Annu. Rev. Ecol. Evol. Syst. 39, 593–613 (2008).
Blouin, M. et al. A review of earthworm impact on soil function and ecosystem services. Eur. J. Soil Sci. 64, 161–182 (2013).
Qiu, J. & Turner, M. G. Effects of non-native Asian earthworm invasion on temperate forest and prairie soils in the Midwestern US. Biol. Invasions 19, 73–88 (2017).
Pejchar, L. & Mooney, H. A. Invasive species, ecosystem services and human well-being. Trends Ecol. Evol. 24, 497–504 (2009).
Viktorov, A. G. Diversity of polyploid races in the family Lumbricidae. Soil Biol. Biochem. 29, 217–221 (1997).
Terhivuo, J. & Saura, A. Dispersal and clonal diversity of North-European parthenogenetic earthworms. Biol. Invasions 8, 1205–1218 (2006).
Garbar, A. V. & Vlasenko, R. P. Karyotypes of three species of the genus Aporrectodea Örley (Oligochaeta: Lumbricidae) from the Ukraine. Comp. Cytogenet. 1, 59–62 (2007).
Bakhtadze, N. G., Bakhtadze, G. I. & Kvavadze, E. S. The chromosome numbers of Georgian earthworms (Oligochaeta: Lumbricidae). Comp. Cytogenet. 2, 79–83 (2008).
Hegarty, M. J. & Hiscock, S. J. Genomic clues to the evolutionary success of polyploid plants. Curr. Biol. 18, R435–R444 (2008).
Finigan, P., Tanurdzic, M. & Martienssen, R. A. in Polyploidy and Genome Evolution (Springer, 2012).
Sailer, C., Schmid, B. & Grossniklaus, U. Apomixis allows the transgenerational fixation of phenotypes in hybrid plants. Curr. Biol. 26, 331–337 (2016).
Novo, M. et al. Multiple introductions and environmental factors affecting the establishment of invasive species on a volcanic island. Soil Biol. Biochem. 85, 89–100 (2015).
Kang, M. M. Earthworm genome assembly protocol. Zenodo https://doi.org/10.5281/zenodo.4288562 (2020).
Lim, J. Y., Yoon, J. & Hovde, C. J. A brief overview of Escherichia coli O157:H7 and its plasmid O157. J. Microbiol. Biotechnol. 20, 5–14 (2010).
van Elsas, J. D., Semenov, A. V., Costa, R. & Trevors, J. T. Survival of Escherichia coli in the environment: fundamental and public health aspects. ISME J. 5, 173–183 (2011).
Lassegues, M., Milochau, A., Doignon, F., Du Pasquier, L. & Valembois, P. Sequence and expression of an Eisenia-fetida-derived cDNA clone that encodes the 40-kDa fetidin antibacterial protein. Eur. J. Biochem. 246, 756–762 (1997).
Rorat, A., Vandenbulcke, F., Galuszka, A., Klimek, B. & Plytycz, B. Protective role of metallothionein during regeneration in Eisenia andrei exposed to cadmium. Comp. Biochem Physiol. 203, 39–50 (2017).
Bilej, M. et al. Distinct carbohydrate recognition domains of an invertebrate defense molecule recognize Gram-negative and Gram-positive bacteria. J. Biol. Chem. 276, 45840–45847 (2001).
Cho, J. H., Park, C. B., Yoon, Y. G., Kim, S. C. & Lumbricin, I. A novel proline-rich antimicrobial peptide from the earthworm: purification, cDNA cloning and molecular characterization. Biochim. Biophys. Acta 1408, 67–76 (1998).
Skanta, F., Prochazkova, P., Roubalova, R., Dvorak, J. & Bilej, M. LBP/BPI homologue in Eisenia andrei earthworms. Dev. Comp. Immunol. 54, 1–6 (2016).
Joskova, R., Silerova, M., Prochazkova, P. & Bilej, M. Identification and cloning of an invertebrate-type lysozyme from Eisenia andrei. Dev. Comp. Immunol. 33, 932–938 (2009).
Prochazkova, P. et al. Developmental and immune role of a novel multiple cysteine cluster TLR from Eisenia andrei earthworms. Front. Immunol. 10, 1277 (2019).
Skanta, F., Roubalova, R., Dvorak, J., Prochazkova, P. & Bilej, M. Molecular cloning and expression of TLR in the Eisenia andrei earthworm. Dev. Comp. Immunol. 41, 694–702 (2013).
Wang, J. et al. Transcriptional responses of earthworm (Eisenia fetida) exposed to naphthenic acids in soil. Environ. Pollut. 204, 264–270 (2015).
Silerova, M. et al. Characterization, molecular cloning and localization of calreticulin in Eisenia fetida earthworms. Gene 397, 169–177 (2007).
Li, Y., Zhao, C., Lu, X., Ai, X. & Qiu, J. Identification of a cytochrome P450 gene in the earthworm Eisenia fetida and its mRNA expression under enrofloxacin stress. Ecotoxicol. Environ. Saf. 150, 70–75 (2018).
Roubalova, R. et al. The effect of dibenzo-p-dioxin- and dibenzofuran-contaminated soil on the earthworm Eisenia andrei. Environ. Pollut. 193, 22–28 (2014).
Weiss, C. L., Pais, M., Cano, L. M., Kamoun, S. & Burbano, H. A. nQuire: a statistical framework for ploidy estimation using next generation sequencing. BMC Bioinform. 19, 122 (2018).
Pendleton, M. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780–786 (2015).
Kokot, M., Dlugosz, M. & Deorowicz, S. KMC 3: counting and manipulating k-mer statistics. Bioinformatics 33, 2759–2761 (2017).
Zwarycz, A. S., Nossa, C. W., Putnam, N. H. & Ryan, J. F. Timing and scope of genomic expansion within Annelida: evidence from homeoboxes in the genome of the earthworm Eisenia fetida. Genome Biol. Evol. 8, 271–281 (2015).
Simakov, O. et al. Insights into bilaterian evolution from three spiralian genomes. Nature 493, 526–531 (2013).
Horn, K. M. et al. Na(+) /K(+) -ATPase gene duplications in clitellate annelids are associated with freshwater colonization. J. Evol. Biol. 32, 580–591 (2019).
Horn, K. M. & Anderson, F. E. Spiralian genomes reveal gene family expansions associated with adaptation to freshwater. J. Mol. Evol. 88, 463–472 (2020).
Schreiber, F., Patricio, M., Muffato, M., Pignatelli, M. & Bateman, A. TreeFam v9: a new website, more species and orthology-on-the-fly. Nucleic Acids Res. 42, D922–D925 (2014).
Li, H. et al. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572–D580 (2006).
Ruan, J. et al. TreeFam: 2008 update. Nucleic Acids Res. 36, D735–D740 (2008).
Han, M. V., Thomas, G. W. C., Lugo-Martinez, J. & Hahn, M. W. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol. Biol. Evol. 30, 1987–1997 (2013).
Hahn, M. W., De Bie, T., Stajich, J. E., Nguyen, C. & Cristianini, N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15, 1153–1160 (2005).
Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).
The Gene Ontology, C. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 47, D330–D338 (2019).
Klopfenstein, D. V. et al. GOATOOLS: a Python library for gene ontology analyses. Sci. Rep. 8, 10872 (2018).
Shao, Y. et al. Genome and single-cell RNA-sequencing of the earthworm Eisenia andrei identifies cellular mechanisms underlying regeneration. Nat. Commun. 11, 2656 (2020).
Liu, X., Sun, Z., Chong, W., Sun, Z. & He, C. Growth and stress responses of the earthworm Eisenia fetida to Escherichia coli O157:H7 in an artificial soil. Micro. Pathog. 46, 266–272 (2009).
Wang, X., Chang, L. & Sun, Z. Differential expression of genes in the earthworm Eisenia fetida following exposure to Escherichia coli O157:H7. Dev. Comp. Immunol. 35, 525–529 (2011).
Wang, X., Chang, L., Sun, Z. & Zhang, Y. Comparative proteomic analysis of differentially expressed proteins in the earthworm Eisenia fetida during Escherichia coli O157:H7 stress. J. Proteome Res. 9, 6547–6560 (2010).
Wang, X., Li, X. & Sun, Z. iTRAQ-based quantitative proteomic analysis of the earthworm Eisenia fetida response to Escherichia coli O157:H7. Ecotoxicol. Environ. Saf. 160, 60–66 (2018).
Zhang, Y. et al. PCR-DGGE analysis of earthworm gut bacteria diversity in stress of Escherichia coli O157:H7. Adv. Biosci. Biotechnol. 4, 437–441 (2013).
Fischer, D. S., Theis, F. J. & Yosef, N. Impulse model-based differential expression analysis of time course sequencing data. Nucleic Acids Res. 46, e119 (2018).
Sander, J., Schultze, J. L. & Yosef, N. ImpulseDE: detection of differentially expressed genes in time series data using impulse models. Bioinformatics 33, 757–759 (2017).
Cooper, E. L. Earthworm immunity. Prog. Mol. Subcell. Biol. 15, 10–45 (1996).
Bilej, M., Prochazkova, P., Silerova, M. & Joskova, R. Earthworm immunity. Adv. Exp. Med Biol. 708, 66–79 (2010).
Langille, M. G. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814–821 (2013).
Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).
Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 9, 559 (2008).
Sapountzis, P. et al. The enterobacterium Trabulsiella odontotermitis presents novel adaptations related to its association with fungus-growing termites. Appl. Environ. Microbiol. 81, 6577–6588 (2015).
Kotak, M. et al. Complete genome sequence of the Opitutaceae bacterium strain TAV5, a potential facultative methylotroph of the wood-feeding termite Reticulitermes flavipes. Genome Announc. https://doi.org/10.1128/genomeA.00060-15 (2015).
Vezina, C., Kudelski, A. & Sehgal, S. N. Rapamycin (AY-22,989), a new antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of the active principle. J. Antibiot. 28, 721–726 (1975).
Jeske, O., Jogler, M., Petersen, J., Sikorski, J. & Jogler, C. From genome mining to phenotypic microarrays: planctomycetes as source for novel bioactive molecules. Antonie Van. Leeuwenhoek 104, 551–567 (2013).
Jeske, O. et al. Developing techniques for the utilization of planctomycetes as producers of bioactive molecules. Front. Microbiol. 7, 1242 (2016).
Kolton, M. et al. Draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi). J. Bacteriol. 194, 5462–5463 (2012).
Kolton, M. et al. Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl. Environ. Microbiol. 77, 4924–4930 (2011).
Sang, M. K. & Kim, K. D. The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. J. Appl. Microbiol. 113, 383–398 (2012).
Youssef, N. H., Blainey, P. C., Quake, S. R. & Elshahed, M. S. Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl. Environ. Microbiol. 77, 7804–7814 (2011).
Havarstein, L. S., Diep, D. B. & Nes, I. F. A family of bacteriocin ABC transporters carry out proteolytic processing of their substrates concomitant with export. Mol. Microbiol. 16, 229–240 (1995).
Weon, H. Y. et al. Rubellimicrobium aerolatum sp. nov., isolated from an air sample in Korea. Int. J. Syst. Evol. Microbiol. 59, 406–410 (2009).
Saha, P. & Chakrabarti, T. Aeromonas sharmana sp. nov., isolated from a warm spring. Int. J. Syst. Evol. Microbiol. 56, 1905–1909 (2006).
Corby-Harris, V. et al. Origin and effect of Alpha 2.2 Acetobacteraceae in honey bee larvae and description of Parasaccharibacter apium gen. nov., sp. nov. Appl. Environ. Microbiol. 80, 7460–7472 (2014).
Ryu, J. H. et al. Innate immune homeostasis by the homeobox gene caudal and commensal-gut mutualism in Drosophila. Science 319, 777–782 (2008).
Cui, H. et al. Bacterial community shaped by heavy metals and contributing to health risks in cornfields. Ecotoxicol. Environ. Saf. 166, 259–269 (2018).
Han, J. I. et al. Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110. J. Bacteriol. 193, 1183–1190 (2011).
Belimov, A. A. et al. Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling. N. Phytol. 181, 413–423 (2009).
Schmalenberger, A. et al. The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimes. Environ. Microbiol. 10, 1486–1500 (2008).
Yurgel, S. N., Douglas, G. M., Dusault, A., Percival, D. & Langille, M. G. I. Dissecting community structure in wild blueberry root and soil microbiome. Front. Microbiol. 9, 1187 (2018).
Zadel, U. et al. Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus. Sci. Total Environ. 711, 134433 (2020).
Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
Sturzenbaum, S. R., Andre, J., Kille, P. & Morgan, A. J. Earthworm genomes, genes and proteins: the (re)discovery of Darwin’s worms. Proc. Biol. Sci. 276, 789–797 (2009).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Marcais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).
English, A. C. et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7, e47768 (2012).
Chaisson, M. J. & Tesler, G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinform. 13, 238 (2012).
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Nishimura, O., Hara, Y. & Kuraku, S. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 33, 3635–3637 (2017).
Liu, B. et al. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. arXiv 1308, 2012v1 (2019).
Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).
Rio, D. C., Ares, M., Hannon, G. J. & Nilsen, T. W. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harb. Protoc. 2010, t5439 (2010).
Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinform. Chapter 4, Unit 4 10, (2004).
Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6, 11 (2015).
Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933–2935 (2013).
Kalvari, I. et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 46, D335–D342 (2018).
Kalvari, I. et al. Non-coding RNA analysis using the Rfam database. Curr. Protoc. Bioinform. 62, e51 (2018).
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).
Apweiler, R. et al. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32, D115–D119 (2004).
Slater, G. S. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinform. 6, 31 (2005).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).
UniProt, C. UniProt: a hub for protein information. Nucleic Acids Res. 43, D204–D212 (2015).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185 (2007).
Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
Huerta-Cepas, J. et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286–D293 (2016).
Howe, K. L., Bolt, B. J., Shafie, M., Kersey, P. & Berriman, M. WormBase ParaSite – a comprehensive resource for helminth genomics. Mol. Biochem. Parasitol. 215, 2–10 (2017).
Barrett, T. et al. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res. 40, D57–D63 (2012).
Howe, K. L. et al. WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res. 44, D774–D780 (2016).
Eddy, S. R. Multiple alignment using hidden Markov models. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 114–120 (1995).
Etherington, G. J., Ramirez-Gonzalez, R. H. & MacLean, D. bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby. Bioinformatics 31, 2565–2567 (2015).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Kuck, P. & Meusemann, K. FASconCAT: convenient handling of data matrices. Mol. Phylogenet. Evol. 56, 1115–1118 (2010).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Sanderson, M. J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301–302 (2003).
Kumar, S., Stecher, G., Suleski, M. & Hedges, S. B. TimeTree: a resource for timelines, timetrees, and divergence times. Mol. Biol. Evol. 34, 1812–1819 (2017).
De Bie, T., Cristianini, N., Demuth, J. P. & Hahn, M. W. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22, 1269–1271 (2006).
Zerbino, D. R. et al. Ensembl 2018. Nucleic Acids Res. 46, D754–D761 (2018).
Pedersen, T. L. MSGFplus: an interface between R and MS-GF+. R package version 1.18.0 (2019).
Gatto, L. & Christoforou, A. Using R and Bioconductor for proteomics data analysis. Biochim. et. Biophys. Acta 1844, 42–51 (2014).
Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahe, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018).
DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).
National Genomics Data Center, M. & Partners. Database resources of the National Genomics Data Center in 2020. Nucleic Acids Res. 48, D24–D33 (2020).
Source: Ecology - nature.com
