Bailey T. L., Johnson J., Grant C. E. and Noble W. S. 2015 The meme suite. Nucleic Acids Res. 43, W39–W49.
Article CAS PubMed PubMed Central Google Scholar
Belinky F., Rot C., Ilan M. and Huchon D. 2008 The complete mitochondrial genome of the demosponge Negombata magnifica (Poecilosclerida). Mol. Phylogenet. Evol. 47, 1238–1243.
Article CAS PubMed Google Scholar
Bolger A. M., Lohse M. and Usadel B. 2014 Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.
Article CAS PubMed PubMed Central Google Scholar
Castresana J. 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552.
Article CAS PubMed Google Scholar
Chan P. P., Lin B. Y., Mak A. J. and Lowe T. M. 2021 tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 49, 9077–9096.
Article CAS PubMed PubMed Central Google Scholar
Desalle R. 2017 MtDNA The small workhorse of evolutionary studies. Front. Biosci. 22, 873–887.
Donath A., Juhling F., Al-Arab M., Bernhart S. H., Reinhardt F., Stadler P. F. et al. 2019 Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Res. 47, 10543–10552.
Article CAS PubMed PubMed Central Google Scholar
Eldem V. and Balcı M. A. 2024 Mining NCBI sequence read archive database: an untapped source of organelle genomes for taxonomic and comparative genomics research. Diversity 16, 104.
Hajdu E., De Paula T. S., Redmond N. E., Cosme B., Collins A. G. and Lobo-Hajdu G. 2013 Mycalina: another crack in the poecilosclerida framework. Integr. Comp. Biol. 53, 462–472.
Jun J., Yu J.-N. and Choi E. H. 2015 Complete mitochondrial genome of Hymeniacidon sinapium (Demospongiae, Halichondriidae). Mitochondrial DNA B 26, 261–262.
Katoh K., Rozewicki J. and Yamada K. D. 2019 MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 20, 1160–1166.
Article CAS PubMed Google Scholar
Kim H., Kim H. J., Jung Y. H., Yu C., An Y. R., Han D. et al. 2017 The complete mitochondrial genome of sponge Halichondria okadai (Demospongiae, Suberitida, Halichondriidae) from Korea water. Mitochondrial DNA B 2, 873–874.
Koboldt D., Steinberg K., Larson D., Wilson R. and Mardis E. R. 2013 The next-generation sequencing revolution and its impact on genomics. Cell 155, 27–38.
Article CAS PubMed PubMed Central Google Scholar
Kozlov A. M., Darriba D., Flouri T., Morel B. and Stamatakis A. 2019 RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455.
Article CAS PubMed PubMed Central Google Scholar
Lavrov D. V. 2010 Rapid proliferation of repetitive palindromic elements in mtDNA of the endemic baikalian sponge Lubomirskia baicalensis. Mol. Biol. Evol. 27, 757–760.
Article CAS PubMed Google Scholar
Lavrov D. V., Wang X. and Kelly M. 2008 Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data. Mol. Phylogenet. Evol. 49, 111–124.
Article CAS PubMed Google Scholar
Lavrov D. V., Diaz M. C., Maldonado M., Morrow C. C., Perez T., Pomponi S. A. et al. 2023 Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera). PLoS One 18, e0287281.
Article CAS PubMed PubMed Central Google Scholar
Lemoine F., Domelevo-Entfellner J.-B., Wilkinson E., Correia D., Davila-Felipe M., De Oliveira T. et al. 2018 Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature 556, 452–456.
Article CAS PubMed PubMed Central Google Scholar
Li D., Liu C.-M., Luo R., Sadakane K. and Lam T.-W. 2015 MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676.
Article CAS PubMed Google Scholar
Linard B., Crampton-Platt A., Moriniere J., Timmermans M. J., Andujar C., Arribas P. et al. 2018 The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera. Mol. Phylogenet. Evol. 128, 1–11.
Article CAS PubMed Google Scholar
Lobry J. R. 1996 Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13, 660–665.
Article CAS PubMed Google Scholar
Pett W. and Lavrov D. V. 2015 Cytonuclear interactions in the evolution of animal mitochondrial tRNA metabolism. Genome Biol. Evol. 7, 2089–2101.
Article CAS PubMed PubMed Central Google Scholar
Plese B., Lukic-Bilela L., Bruvo-Maaric B., Harcet M., Imesek M., Bilandzija H. et al. 2012 The mitochondrial genome of stygobitic sponge Eunapius subterraneus: mtDNA is highly conserved in fresh311 water sponges. Hydrobiologia 687, 49–59.
Plese B., Rossi M. E., Kenny N. J., Taboada S., Koutsouveli V. and Riesgo A. 2019 Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species. Mol. Ecol. Resour. 19, 1230–1239.
Article CAS PubMed Google Scholar
Redmond N. E., Morrow C. C., Thacker R. W., Diaz M. C., Boury-Esnault N., Cardenas P. et al. 2013 Phylogeny and systematics of demospongiae in light of new small-subunit ribosomal DNA (18S) sequences. Integr. Comp. Biol. 53, 388–415.
Article CAS PubMed Google Scholar
Rubin-Blum M., Antony C. P., Sayavedra L., Martínez-Perez C., Birgel D., Peckmann J. et al. 2019 Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts. ISME J. 13, 1209–1225.
Article CAS PubMed PubMed Central Google Scholar
Satam H., Joshi K., Mangrolia U., Waghoo S., Zaidi G., Rawool S. et al. 2023 Next-generation sequencing technology: current trends and advancements. Biology 12, 997.
Article CAS PubMed PubMed Central Google Scholar
Stephens Z. D., Lee S. Y., Faghri F., Campbell R. H., Zhai C., Efron M. J. et al. 2015 Big data: astronomical or genomical? PLoS Biol. 13, e1002195.
Article PubMed PubMed Central Google Scholar
Stothard P. 2000 The Sequence manipulation suite: javascript programs for analyzing and formatting protein and DNA sequences. BioTechniques 28, 1102–1104.
Article CAS PubMed Google Scholar
Stothard P. and Wishart D. S. 2005 Circular genome visualization and exploration using CGView. Bioinformatics 21, 537–539.
Article CAS PubMed Google Scholar
Thacker R. W., Hill A. L., Hill M. S., Redmond N. E., Collins A. G., Morrow C. C. et al. 2013 Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution. Integr. Comp. Biol. 53, 373–387.
Comments (0)