Ribosomal ITS Sequences Allow Resolution of Freshwater Sponge Phylogeny with Alignments Guided by Secondary Structure Prediction

Overview

Journal J Mol Evol

Specialty Biochemistry

Date 2008 Nov 15

PMID 19009316

Citations 6

Authors

Valeria Itskovich

Andrey Gontcharov

Yoshiki Masuda

Tsutomu Nohno

Sergey Belikov

Sofia Efremova

Martin Meixner

Dorte Janussen

Affiliations

Soon will be listed here.

Abstract

Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.

Citing Articles

The complete mitochondrial genome of (Lubomirskiidae): description and phylogenetic analysis.

Maikova O, Sherbakov D, Belikov S Mitochondrial DNA B Resour. 2021; 1(1):569-570.

PMID: 33490409 PMC: 7801006. DOI: 10.1080/23802359.2016.1172273.

Genetic analysis confirms the freshwater origin of the endemic Caspian sponges (Demospongiae, Spongillida, Metschnikowiidae).

Sokolova A, Palatov D, Itskovich V Zookeys. 2020; 915:1-16.

PMID: 32148420 PMC: 7052039. DOI: 10.3897/zookeys.915.47460.

A new species of Baikal endemic sponges (Porifera, Demospongiae, Spongillida, Lubomirskiidae).

Bukshuk N, Maikova O Zookeys. 2020; 906:113-130.

PMID: 32021558 PMC: 6989567. DOI: 10.3897/zookeys.906.39534.

Intragenomic Profiling Using Multicopy Genes: The rDNA Internal Transcribed Spacer Sequences of the Freshwater Sponge Ephydatia fluviatilis.

Karlep L, Reintamm T, Kelve M PLoS One. 2013; 8(6):e66601.

PMID: 23825547 PMC: 3688955. DOI: 10.1371/journal.pone.0066601.

Comparative evolution of S7 Intron 1 and ribosomal internal transcribed spacer in Coilia nasus (Clupeiformes: Engraulidae).

Liu D, Guo H, Tang W, Yang J Int J Mol Sci. 2012; 13(3):3085-3100.

PMID: 22489143 PMC: 3317704. DOI: 10.3390/ijms13033085.

References

Coleman A, Maria Preparata R, Mehrotra B, Mai J . Derivation of the Secondary Structure of the ITS-1 Transcript in Volvocales and its Taxonomic Correlations. Protist. 2012; 149(2):135-46. DOI: 10.1016/S1434-4610(98)70018-5. View

Coleman A . Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res. 2007; 35(10):3322-9. PMC: 1904279. DOI: 10.1093/nar/gkm233. View

Duran S, Giribet G, Turon X . Phylogeographical history of the sponge Crambe crambe (Porifera, Poecilosclerida): range expansion and recent invasion of the Macaronesian islands from the Mediterranean Sea. Mol Ecol. 2003; 13(1):109-22. DOI: 10.1046/j.1365-294x.2003.02022.x. View

Bargues M, Vigo M, Horak P, Dvorak J, Patzner R, Pointier J . European Lymnaeidae (Mollusca: Gastropoda), intermediate hosts of trematodiases, based on nuclear ribosomal DNA ITS-2 sequences. Infect Genet Evol. 2003; 1(2):85-107. DOI: 10.1016/s1567-1348(01)00019-3. View

Zuker M . Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31(13):3406-15. PMC: 169194. DOI: 10.1093/nar/gkg595. View

Meixner M, Luter C, Eckert C, Itskovich V, Janussen D, von Rintelen T . Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes. Mol Phylogenet Evol. 2007; 45(3):875-86. DOI: 10.1016/j.ympev.2007.09.007. View

Coleman A . ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet. 2003; 19(7):370-5. DOI: 10.1016/S0168-9525(03)00118-5. View

Posada D, Crandall K . MODELTEST: testing the model of DNA substitution. Bioinformatics. 1999; 14(9):817-8. DOI: 10.1093/bioinformatics/14.9.817. View

Felsenstein J . CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP. Evolution. 2017; 39(4):783-791. DOI: 10.1111/j.1558-5646.1985.tb00420.x. View

10.

Wolf M, Achtziger M, Schultz J, Dandekar T, Muller T . Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA. 2005; 11(11):1616-23. PMC: 1370847. DOI: 10.1261/rna.2144205. View

11.

Goertzen L, Cannone J, Gutell R, Jansen R . ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. Mol Phylogenet Evol. 2003; 29(2):216-34. DOI: 10.1016/s1055-7903(03)00094-0. View

12.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

13.

Schmitt S, Hentschel U, Zea S, Dandekar T, Wolf M . ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). J Mol Evol. 2005; 60(3):327-36. DOI: 10.1007/s00239-004-0162-0. View

14.

Kimura M . A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980; 16(2):111-20. DOI: 10.1007/BF01731581. View

15.

Bargues M, Horak P, Patzner R, Pointier J, Jackiewicz M, Meier-Brook C . Insights into the relationships of Palearctic and Nearctic lymnaeids (Mollusca: Gastropoda) by rDNA ITS-2 sequencing and phylogeny of stagnicoline intermediate host species of Fasciola hepatica. Parasite. 2003; 10(3):243-55. DOI: 10.1051/parasite/2003103243. View

16.

Yoon H, Lee J, Boo S, Bhattacharya D . Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyceae) based on plastid-encoded RuBisCo spacer and nuclear-encoded ITS sequence comparisons. Mol Phylogenet Evol. 2001; 21(2):231-43. DOI: 10.1006/mpev.2001.1009. View

17.

Joseph N, Krauskopf E, Vera M, Michot B . Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res. 1999; 27(23):4533-40. PMC: 148739. DOI: 10.1093/nar/27.23.4533. View

18.

Gustincich S, Manfioletti G, Del Sal G, Schneider C, Carninci P . A fast method for high-quality genomic DNA extraction from whole human blood. Biotechniques. 1991; 11(3):298-300, 302. View

19.

Coleman A, Vacquier V . Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). J Mol Evol. 2002; 54(2):246-57. DOI: 10.1007/s00239-001-0006-0. View

20.

Zubakov D, Shcherbakov D, Sitnikova T . [Analysis of phylogeny of endemic mollusca of family Baicaliidae, Clessin 1878 (Gastropoda, Pectinibranchia) from Baical lake using fragments of nucleotide sequences of the mitochondrial gene CO1]. Mol Biol (Mosk). 1998; 31(6):1092-7. View