Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates
Abstract
:1. Introduction
2. Results
2.1. Study of Model Strains
2.2. Study of Marine Invertebrate Microbiome Samples
2.2.1. Taxonomy of Source Material
2.2.2. Sequencing and Assembly of Marine Invertebrate MDA Amplified Metagenomes
2.2.3. Taxonomic Profiles
2.2.4. Annotation of Genes and Enzymes
2.2.5. Biosynthetic Gene Clusters
3. Discussion
4. Materials and Methods
4.1. Sampling and Sample Preparations
Taxonomic Identification of Sponge Source Material
4.2. Separation of Bacteria-Sized Cells from Homogenized Invertebrate Tissue
4.3. Estimation of Bacteria Concentration
4.4. Multiple Displacement Amplification
4.5. Illumina MiSeq Sequencing
4.6. Analysis of Sequence Data
4.7. Model Experiment
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Vuong, P.; Wise, M.J.; Whiteley, A.S.; Kaur, P. Small investments with big returns: Environmental genomic bioprospecting of microbial life. Crit. Rev. Microbiol. 2022, 48, 641–655. [Google Scholar] [CrossRef] [PubMed]
- Sysoev, M.; Grötzinger, S.W.; Renn, D.; Eppinger, J.; Rueping, M.; Karan, R. Bioprospecting of novel extremozymes from prokaryotes—The advent of culture-independent methods. Front. Microbiol. 2021, 12, 630013. [Google Scholar] [CrossRef] [PubMed]
- Cuadrat, R.R.C.; Ionescu, D.; Dávila, A.M.R.; Grossart, H.-P. Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics. Front. Microbiol. 2018, 9, 251. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Singleton, C.M.; Petriglieri, F.; Kristensen, J.M.; Kirkegaard, R.H.; Michaelsen, T.Y.; Andersen, M.H.; Kondrotaite, Z.; Karst, S.M.; Dueholm, M.S.; Nielsen, P.H.; et al. Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing. Nat. Commun. 2021, 12, 2009. [Google Scholar] [CrossRef]
- Rubio-Portillo, E.; Martin-Cuadrado, A.-B.; Ramos-Esplá, A.Á.; Antón, J.; Raina, J.-B. Metagenomics unveils Posidonia oceanica “Banquettes” as a potential source of novel bioactive compounds and carbohydrate active enzymes (CAZymes). mSystems 2021, 6, e00866-21. [Google Scholar] [CrossRef]
- Probst, A.J.; Weinmaier, T.; DeSantis, T.Z.; Santo Domingo, J.W.; Ashbolt, N. New perspectives on microbial community distortion after whole-genome amplification. PLoS ONE 2015, 10, e0124158. [Google Scholar] [CrossRef] [Green Version]
- James, G.L.; Latif, M.T.; Isa, M.N.M.; Bakar, M.F.A.; Yusuf, N.Y.M.; Broughton, W.; Murad, A.M.; Abu Bakar, F.D. Metagenomic datasets of air samples collected during episodes of severe smoke-haze in Malaysia. Data Brief 2021, 36, 107124. [Google Scholar] [CrossRef]
- Stocker, R. Marine microbes see a sea of gradients. Science 2012, 338, 628–633. [Google Scholar] [CrossRef] [Green Version]
- Liu, N.; Yan, X.; Zhang, M.; Xie, L.; Wang, Q.; Huang, Y.; Zhou, X.; Wang, S.; Zhou, Z. Microbiome of Fungus-Growing Termites: A New Reservoir for Lignocellulase Genes. Appl. Environ. Microbiol. 2011, 77, 48–56. [Google Scholar] [CrossRef] [Green Version]
- Mitrović, J.; Siewert, C.; Duduk, B.; Hecht, J.; Mölling, K.; Broecker, F.; Beyerlein, P.; Büttner, C.; Bertaccini, A.; Kube, M. Generation and Analysis of Draft Sequences of ‘Stolbur’ Phytoplasma from Multiple Displacement Amplification Templates. Microb. Physiol. 2014, 24, 1–11. [Google Scholar] [CrossRef]
- Steinert, G.; Rohde, S.; Janussen, D.; Blaurock, C.; Schupp, P.J. Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks. Sci. Rep. 2017, 7, 2542. [Google Scholar] [CrossRef] [Green Version]
- Yokouchi, H.; Fukuoka, Y.; Mukoyama, D.; Calugay, R.; Takeyama, H.; Matsunaga, T. Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using ϕ29 polymerase. Environ. Microbiol. 2006, 8, 1155–1163. [Google Scholar] [CrossRef]
- Wegley, L.; Edwards, R.; Rodriguez-Brito, B.; Liu, H.; Rohwer, F. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ. Microbiol. 2007, 9, 2707–2719. [Google Scholar] [CrossRef]
- Hosono, S.; Faruqi, A.F.; Dean, F.B.; Du, Y.; Sun, Z.; Wu, X.; Du, J.; Kingsmore, S.F.; Egholm, M.; Lasken, R.S. Unbiased whole-genome amplification directly from clinical samples. Genome Res. 2003, 13, 954–964. [Google Scholar] [CrossRef] [Green Version]
- Raghunathan, A.; Ferguson, H.R., Jr.; Bornarth, C.J.; Song, W.; Driscoll, M.; Lasken, R.S. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 2005, 71, 3342–3347. [Google Scholar] [CrossRef] [Green Version]
- Abulencia, C.B.; Wyborski, D.L.; Garcia, J.A.; Podar, M.; Chen, W.; Chang, S.H.; Chang, H.W.; Watson, D.; Brodie, E.L.; Hazen, T.C.; et al. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl. Environ. Microbiol. 2006, 72, 3291–3301. [Google Scholar] [CrossRef] [Green Version]
- Woyke, T.; Xie, G.; Copeland, A.; González, J.M.; Han, C.; Kiss, H.; Saw, J.H.; Senin, P.; Yang, C.; Chatterji, S.; et al. Assembling the marine metagenome, one cell at a time. PLoS ONE 2009, 4, e5299. [Google Scholar] [CrossRef]
- Binga, E.K.; Lasken, R.S.; Neufeld, J.D. Something from (almost) nothing: The impact of multiple displacement amplification on microbial ecology. ISME J. 2008, 2, 233–241. [Google Scholar] [CrossRef] [Green Version]
- Ellegaard, K.M.; Klasson, L.; Andersson, S.G.E. Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations. PLoS ONE 2013, 8, e82319. [Google Scholar] [CrossRef]
- Nurk, S.; Bankevich, A.; Antipov, D.; Gurevich, A.A.; Korobeynikov, A.; Lapidus, A.; Prjibelski, A.D.; Pyshkin, A.; Sirotkin, A.; Sirotkin, Y.; et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J. Comput. Biol. 2013, 20, 714–737. [Google Scholar] [CrossRef] [Green Version]
- Marine, R.; McCarren, C.; Vorrasane, V.; Nasko, D.; Crowgey, E.; Polson, S.W.; Wommack, K.E. Caught in the middle with multiple displacement amplification: The myth of pooling for avoiding multiple displacement amplification bias in a metagenome. Microbiome 2014, 2, 3. [Google Scholar] [CrossRef] [Green Version]
- Ahsanuddin, S.; Afshinnekoo, E.; Gandara, J.; Hakyemezoğlu, M.; Bezdan, D.; Minot, S.; Greenfield, N.; Mason, C.E. Assessment of REPLI-g multiple displacement whole genome amplification (WGA) techniques for metagenomic applications. J. Biomol. Tech. 2017, 28, 46–55. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zong, C.; Lu, S.; Chapman, A.R.; Xie, X.S. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 2012, 338, 1622–1626. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Wu, Y.; Dai, Y.; Liu, G.; Zeng, J.; Lin, X. Assessment of two whole genome amplification techniques in terms of soil community profiles. Appl. Soil Ecol. 2020, 150, 103455. [Google Scholar] [CrossRef]
- Brinkmann, C.M.; Marker, A.; Kurtböke, D.I. An overview on marine sponge-symbiotic bacteria as unexhausted sources for natural product discovery. Diversity 2017, 9, 40. [Google Scholar] [CrossRef] [Green Version]
- Lackner, G.; Peters, E.E.; Helfrich, E.J.N.; Piel, J. Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. Proc. Nat. Acad. Sci. USA 2017, 114, E347–E356. [Google Scholar] [CrossRef] [Green Version]
- de Oliveira, B.F.R.; Carr, C.M.; Dobson, A.D.W.; Laport, M.S. Harnessing the sponge microbiome for industrial biocatalysts. Appl. Microbiol. Biotechnol. 2020, 104, 8131–8154. [Google Scholar] [CrossRef]
- Hentschel, U.; Piel, J.; Degnan, S.M.; Taylor, M.W. Genomic insights into the marine sponge microbiome. Nat. Rev. Microbiol. 2012, 10, 641–654. [Google Scholar] [CrossRef]
- Woyke, T.; Doud, D.F.R.; Schulz, F. The trajectory of microbial single-cell sequencing. Nat. Meth. 2017, 14, 1045–1054. [Google Scholar] [CrossRef]
- Kennedy, J.; Codling, C.E.; Jones, B.V.; Dobson, A.D.W.; Marchesi, J.R. Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environ. Microbiol. 2008, 10, 1888–1902. [Google Scholar] [CrossRef]
- Sudan, A.K.; Vakhlu, J. Isolation of a thioesterase gene from the metagenome of a mountain peak, Apharwat, in the northwestern Himalayas. 3 Biotech 2013, 3, 19–27. [Google Scholar] [CrossRef] [Green Version]
- Vester, J.K.; Glaring, M.A.; Stougaard, P. Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing. Microb. Cell Fact. 2014, 13, 72. [Google Scholar] [CrossRef] [Green Version]
- Tan, S.M.; Yung, P.Y.M.; Hutchinson, P.E.; Xie, C.; Teo, G.H.; Ismail, M.H.; Drautz-Moses, D.I.; Little, P.F.R.; Williams, R.B.H.; Cohen, Y. Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities. NPJ Biofilms Microbiomes 2019, 5, 17. [Google Scholar] [CrossRef] [Green Version]
- Grieb, A.; Bowers, R.M.; Oggerin, M.; Goudeau, D.; Lee, J.; Malmstrom, R.R.; Woyke, T.; Fuchs, B.M. A pipeline for targeted metagenomics of environmental bacteria. Microbiome 2020, 8, 21. [Google Scholar] [CrossRef]
- Medema, M.H.; Blin, K.; Cimermancic, P.; de Jager, V.; Zakrzewski, P.; Fischbach, M.A.; Weber, T.; Takano, E.; Breitling, R. antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucl. Acids Res. 2011, 39, W339–W346. [Google Scholar] [CrossRef]
- Klassen, J.L.; Currie, C.R. Gene fragmentation in bacterial draft genomes: Extent, consequences and mitigation. BMC Genom. 2012, 13, 14. [Google Scholar] [CrossRef] [Green Version]
- Goldstein, S.; Beka, L.; Graf, J.; Klassen, J.L. Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing. BMC Genom. 2019, 20, 23. [Google Scholar] [CrossRef] [Green Version]
- Xu, G.; Zhang, L.; Liu, X.; Guan, F.; Xu, Y.; Yue, H.; Huang, J.-Q.; Chen, J.; Wu, N.; Tian, J. Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome. BMC Genom. 2022, 23, 37. [Google Scholar] [CrossRef]
- Lasken, R.S. Single-cell genomic sequencing using multiple displacement amplification. Curr. Opin. Microbiol. 2007, 10, 510–516. [Google Scholar] [CrossRef]
- Oxford Nanopore Technologies. Ligation Sequencing gDNA—Whole Genome Amplification (SQK-LSK112); Version: WAL_9154_V112_REVF_09FEB2022; 2022. Available online: https://community.nanoporetech.com/docs/prepare/library_prep_protocols/premium-whole-genome-amplification-sqk-lsk112/v/wal_9154_v112_revf_09feb2022 (accessed on 15 November 2022).
- Strehlow, B.W.; Schuster, A.; Francis, W.R.; Canfield, D.E. Metagenomic data for Halichondria panicea from Illumina and nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts. BMC Res. Notes 2022, 15, 135. [Google Scholar] [CrossRef]
- Kiguchi, Y.; Nishijima, S.; Kumar, N.; Hattori, M.; Suda, W. Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads. DNA Res. 2021, 28, dsab019. [Google Scholar] [CrossRef] [PubMed]
- Uppal, S.; Metz, J.L.; Xavier, R.K.M.; Nepal, K.K.; Xu, D.; Wang, G.; Kwan, J.C. Uncovering Lasonolide A biosynthesis using genome-resolved metagenomics. mBio 2022, 13, e01524-22. [Google Scholar] [CrossRef] [PubMed]
- Fieseler, L.; Quaiser, A.; Schleper, C.; Hentschel, U. Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics. Environ. Microbiol. 2006, 8, 612–624. [Google Scholar] [CrossRef] [PubMed]
- Ponnudurai, R.; Sayavedra, L.; Kleiner, M.; Heiden, S.E.; Thürmer, A.; Felbeck, H.; Schlüter, R.; Sievert, S.M.; Daniel, R.; Schweder, T.; et al. Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont. Stand. Genomic Sci. 2017, 12, 50. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Robbins, S.J.; Song, W.; Engelberts, J.P.; Glasl, B.; Slaby, B.M.; Boyd, J.; Marangon, E.; Botté, E.S.; Laffy, P.; Thomas, T.; et al. A genomic view of the microbiome of coral reef demosponges. ISME J. 2021, 15, 1641–1654. [Google Scholar] [CrossRef]
- Knobloch, S.; Johannsson, R.; Marteinsson, V. Bacterial diversity in the marine sponge Halichondria panicea from Icelandic waters and host-specificity of its dominant symbiont “Candidatus Halichondribacter symbioticus”. FEMS Microbiol. Ecol. 2019, 95, fiy220. [Google Scholar] [CrossRef]
- Naim, M.A.; Morillo, J.A.; Sørensen, S.J.; Waleed, A.A.-S.; Smidt, H.; Sipkema, D. Host-specific microbial communities in three sympatric North Sea sponges. FEMS Microbiol. Ecol. 2014, 90, 390–403. [Google Scholar] [CrossRef] [Green Version]
- Rusanova, A.; Fedorchuk, V.; Toshchakov, S.; Dubiley, S.; Sutormin, D. An interplay between viruses and bacteria associated with the White Sea sponges revealed by metagenomics. Life 2022, 12, 25. [Google Scholar] [CrossRef]
- Knobloch, S.; Jóhannsson, R.; Marteinsson, V. Co-cultivation of the marine sponge Halichondria panicea and its associated microorganisms. Sci. Rep. 2019, 9, 10403. [Google Scholar] [CrossRef] [Green Version]
- Graça, A.P.; Calisto, R.; Lage, O.M. Planctomycetes as novel source of bioactive molecules. Front. Microbiol. 2016, 7, 1241. [Google Scholar] [CrossRef] [Green Version]
- Calisto, R.; Sæbø, E.F.; Storesund, J.E.; Øvreås, L.; Herfindal, L.; Lage, O.M. Anticancer activity in Planctomycetes. Front. Mar. Sci. 2019, 5, 499. [Google Scholar] [CrossRef]
- Fuerst, J.A.; Sagulenko, E. Beyond the bacterium: Planctomycetes challenge our concepts of microbial structure and function. Nat. Rev. Microbiol. 2011, 9, 403–413. [Google Scholar] [CrossRef] [PubMed]
- Morrow, C.C.; Picton, B.E.; Erpenbeck, D.; Boury-Esnault, N.; Maggs, C.A.; Allcock, A.L. Congruence between nuclear and mitochondrial genes in Demospongiae: A new hypothesis for relationships within the G4 clade (Porifera: Demospongiae). Mol. Phylogen. Evol. 2012, 62, 174–190. [Google Scholar] [CrossRef] [PubMed]
- Plotkin, A.; Voigt, O.; Willassen, E.; Rapp, H.T. Molecular phylogenies challenge the classification of Polymastiidae (Porifera, Demospongiae) based on morphology. Org. Divers. Evol. 2017, 17, 45–66. [Google Scholar] [CrossRef] [Green Version]
- Meyer, C.P. Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biol. J. Linnean Soc. 2003, 79, 401–459. [Google Scholar] [CrossRef] [Green Version]
- Oberacker, P.; Stepper, P.; Bond, D.M.; Höhn, S.; Focken, J.; Meyer, V.; Schelle, L.; Sugrue, V.J.; Jeunen, G.-J.; Moser, T.; et al. Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation. PLoS Biol. 2019, 17, e3000107. [Google Scholar] [CrossRef] [Green Version]
- Noble, R.T.; Fuhrman, J.A. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 1998, 14, 113–118. [Google Scholar] [CrossRef] [Green Version]
- Patel, A.; Noble, R.T.; Steele, J.A.; Schwalbach, M.S.; Hewson, I.; Fuhrman, J.A. Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat. Protoc. 2007, 2, 269–276. [Google Scholar] [CrossRef] [Green Version]
- Arkin, A.P.; Cottingham, R.W.; Henry, C.S.; Harris, N.L.; Stevens, R.L.; Maslov, S.; Dehal, P.; Ware, D.; Perez, F.; Canon, S.; et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat. Biotechnol. 2018, 36, 566. [Google Scholar] [CrossRef] [Green Version]
- Menzel, P.; Ng, K.L.; Krogh, A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 2016, 7, 11257. [Google Scholar] [CrossRef] [Green Version]
- Klemetsen, T.; Raknes, I.A.; Fu, J.; Agafonov, A.; Balasundaram, S.V.; Tartari, G.; Robertsen, E.; Willassen, N.P. The MAR databases: Development and implementation of databases specific for marine metagenomics. Nucl. Acids Res. 2017, 46, D692–D699. [Google Scholar] [CrossRef]
- Andrews, S. FastQC—A Quality Control Tool for High Throughput Sequence Data. Available online: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 13 November 2022).
- Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef] [Green Version]
- Aronesty, E. Ea-Utils: “Command-Line Tools for Processing Biological Sequencing Data”. Available online: https://github.com/ExpressionAnalysis/ea-utils (accessed on 13 November 2022).
- Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef] [Green Version]
- Nurk, S.; Meleshko, D.; Korobeynikov, A.; Pevzner, P.A. metaSPAdes: A new versatile metagenomic assembler. Genome Res. 2017, 27, 824–834. [Google Scholar] [CrossRef] [Green Version]
- Gurevich, A.; Saveliev, V.; Vyahhi, N.; Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 2013, 29, 1072–1075. [Google Scholar] [CrossRef] [Green Version]
- Langmead, B.; Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9, 357–359. [Google Scholar] [CrossRef] [Green Version]
- Seemann, T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 2014, 30, 2068–2069. [Google Scholar] [CrossRef] [Green Version]
- Blin, K.; Shaw, S.; Steinke, K.; Villebro, R.; Ziemert, N.; Lee, S.Y.; Medema, M.H.; Weber, T. antiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline. Nucl. Acids Res. 2019, 47, W81–W87. [Google Scholar] [CrossRef] [Green Version]
BS1 | BS2 | EC1 | EC2 | VA1 | VA2 | VA3 | VA4 | VA5 | VA6 | |
---|---|---|---|---|---|---|---|---|---|---|
Total genome fraction (%) | 74.5 | 59.0 | 66.7 | 89.0 | 83.2 | 50.3 | 63.2 | 2.3 | 43.1 | 90.4 |
Total alignment (kbp) | 3491 | 2907 | 3553 | 4536 | 4176 | 3106 | 3267 | 143 | 2212 | 4598 |
Largest alignment (kbp) | 136.0 | 46.9 | 126.1 | 102.6 | 121.2 | 65.1 | 55.2 | 11.2 | 18.3 | 69.5 |
Unaligned fraction (%) | 3.7 | 4.9 | 3.9 | 3.4 | 2.6 | 6.1 | 5.0 | 51.0 | 12.6 | 2.7 |
Total length (kbp) | 3626 | 3057 | 3698 | 4694 | 4287 | 3309 | 3437 | 292 | 2531 | 4724 |
#Contigs (≥1000 bp) | 453 | 429 | 332 | 378 | 514 | 541 | 570 | 86 | 665 | 465 |
#Contigs (≥10,000 bp) | 94 | 87 | 84 | 127 | 122 | 83 | 86 | 2 | 18 | 139 |
largest contig (kbp) | 136.1 | 60.3 | 181.0 | 102.6 | 121.2 | 130.0 | 55.2 | 13.2 | 26.3 | 69.6 |
N50 | 15,245 | 12,593 | 30,060 | 30,064 | 14,895 | 9276 | 8952 | 1914 | 2604 | 20,874 |
Mean sequencing coverage | 56.8 | 93.8 | 68.1 | 68.0 | 60.5 | 59.2 | 77.6 | 493.6 | 38.1 | 52.8 |
Standard deviation | 111.9 | 176.5 | 99.5 | 105.9 | 105.7 | 140.1 | 188.2 | 1346.0 | 416.2 | 92.8 |
Number of protein-coding genes | 3520 | 2988 | 3464 | 4377 | 3659 | 2883 | 2988 | 236 | 2174 | 4092 |
Average protein length (aa) | 265 | 254 | 284 | 291 | 293 | 271 | 275 | 167 | 221 | 298 |
Mix 1 | Mix 2 | Mix 3 | Mix 4 | Mix 5 | Mix 6 | Mix 7 | Mix 8 | |
---|---|---|---|---|---|---|---|---|
Total genome fraction (%) | 67.6 | 66.1 | 50.5 | 50.9 | 42.8 | 39.9 | 67.1 | 52.1 |
E. coli | 95.6 | 95.3 | 93.4 | 84.2 | 92.0 | 91.8 | 95.1 | 95.9 |
B. subtilis | 37.4 | 37.9 | 17.6 | 67.7 | 26.3 | 10.0 | 61.2 | 26.8 |
V. atlanticus | 65.6 | 61.8 | 37.5 | 4.7 | 9.8 | 16.2 | 44.6 | 31.4 |
Total alignment (kbp) | 9535 | 9119 | 6954 | 7082 | 5893 | 5556 | 9229 | 7270 |
Largest alignment (kbp): | ||||||||
E. coli | 223.9 | 258.4 | 155.5 | 68.7 | 107.4 | 78.4 | 173.6 | 217.9 |
B. subtilis | 61.0 | 17.4 | 23.4 | 39.2 | 25.6 | 11.8 | 33.2 | 18.2 |
V. atlanticus | 64.6 | 45.4 | 45.6 | 12.6 | 15.5 | 9.9 | 24.8 | 29.7 |
Unaligned fraction | 1.1 | 1.2 | 1.3 | 1.3 | 1.6 | 1.6 | 1.1 | 1.2 |
Total length (kbp) | 9642 | 9232 | 7048 | 7175 | 5991 | 5646 | 9328 | 7360 |
#Contigs (≥1000 bp) | 1147 | 1280 | 791 | 1044 | 692 | 736 | 1287 | 825 |
#Contigs (≥10,000 bp) | 150 | 124 | 127 | 183 | 122 | 129 | 160 | 84 |
Largest contig (kbp) | 233.9 | 259.0 | 160.4 | 68.7 | 132.8 | 89.4 | 173.6 | 218.0 |
N50 | 26,721 | 16,815 | 27,496 | 11,101 | 22,467 | 18,168 | 15,283 | 47,972 |
Mean sequencing coverage | 40.0 | 35.6 | 45.2 | 43.3 | 49.0 | 48.8 | 40.2 | 48.1 |
Standard deviation of sequencing cover | 56.8 | 44.9 | 57.6 | 69.2 | 66.3 | 67.4 | 57.9 | 59.2 |
Number of protein-coding genes | 8872 | 8491 | 6473 | 7043 | 5720 | 5276 | 8658 | 6772 |
Average protein length (aa) | 277 | 267 | 280 | 262 | 272 | 273 | 271 | 269 |
Sample | Origin | Taxonomic inference |
---|---|---|
A | Sponge fragment | Order Poecilosclerida * |
B | Sponge | Halichondria panicea * |
C | Sponge | Order Poecilosclerida * |
D | Sponge fragment | Family Myxillidae * |
E | Bryozoa | Alcyonidium gelatinosum |
F | Sponge | Genus Myxilla * |
Sample | Estimated # Cells | Total Length (kbp) | Largest Contig (kbp) | N50 | # Contigs | # Contigs (>10,000 bp) | Sequencing Coverage | SD |
---|---|---|---|---|---|---|---|---|
A1 | 2 | 5867 | 34.3 | 3992 | 1717 | 78 | 59.3 | 198.5 |
A2 | 2 | 8179 | 27.2 | 4005 | 2393 | 99 | 60.8 | 197.9 |
A3 | 170 | 31,262 | 68.6 | 1715 | 11,673 | 437 | 8.0 | 11.9 |
A4 | 170 | 33,557 | 168.3 | 2011 | 10,984 | 480 | 8.4 | 14.0 |
B1 | 75 | 29,443 | 106.9 | 1815 | 10,708 | 396 | 5.9 | 26.8 |
B2 | 75 | 30,326 | 102.2 | 1794 | 11,256 | 387 | 6.4 | 22.0 |
B3 | 375 | 24,807 | 124.5 | 1533 | 10,002 | 226 | 5.6 | 23.8 |
C1 | 26 | 8588 | 41.0 | 3851 | 2483 | 156 | 34.6 | 99.4 |
C2 | 54 | 17,962 | 89.4 | 2264 | 5830 | 277 | 12.5 | 35.4 |
D1 | 7 | 19,116 | 66.1 | 2093 | 6617 | 278 | 9.2 | 42.7 |
E1 | 2 | 5193 | 30.1 | 3421 | 1642 | 54 | 43.6 | 150.7 |
E2 | 425 | 15,303 | 40.2 | 1205 | 6246 | 161 | 6.4 | 25.1 |
E3 | 850 | 4520 | 29.8 | 3655 | 1408 | 47 | 107.0 | 292.4 |
F1 | 2 | 24,272 | 98.6 | 3378 | 7056 | 423 | 9.6 | 19.5 |
A1 | A2 | A3 | A4 | B1 | B2 | B3 | C1 | C2 | D1 | E1 | E2 | E3 | F1 | Total | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Triacylglycerol lipase | EC 3.1.1.3 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 8 | |||||||
Protease | EC 3.4 | 34 | 42 | 136 | 169 | 125 | 129 | 95 | 32 | 70 | 72 | 27 | 75 | 20 | 121 | 1147 |
Chitinase | EC 3.2.1.14 | 1 | 1 | 1 | 1 | 4 | ||||||||||
Alpha-amylase | EC 3.2.1.1 | 3 | 4 | 2 | 9 | |||||||||||
Cellulase | EC 3.2.1.4 | 1 | 1 | 2 | ||||||||||||
Lysozyme | EC 3.2.1.17 | 1 | 5 | 5 | 4 | 2 | 17 | |||||||||
Xylanase | EC 3.2.1.8/32 | 4 | 4 | 2 | 1 | 11 | ||||||||||
Xylosidase | EC 3.2.1.37/72 | 2 | 2 | 3 | 7 | |||||||||||
DNA ligase (ATP) | EC 6.5.1.1 | 1 | 1 | 7 | 10 | 8 | 12 | 8 | 2 | 7 | 8 | 1 | 3 | 68 | ||
DNA ligase (NAD+) | EC 6.5.1.2 | 3 | 2 | 13 | 24 | 14 | 9 | 12 | 2 | 7 | 5 | 2 | 8 | 2 | 9 | 112 |
RNA 3’-terminal-phosphate cyclase (ATP) | EC 6.5.1.4 | 1 | 1 | 1 | 2 | 5 |
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Elvheim, A.I.; Li, C.; Landfald, B. Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Mar. Drugs 2023, 21, 165. https://doi.org/10.3390/md21030165
Elvheim AI, Li C, Landfald B. Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Marine Drugs. 2023; 21(3):165. https://doi.org/10.3390/md21030165
Chicago/Turabian StyleElvheim, Andrea Iselin, Chun Li, and Bjarne Landfald. 2023. "Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates" Marine Drugs 21, no. 3: 165. https://doi.org/10.3390/md21030165