92 results on '"Lavrov, Dennis V."'
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52. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages
- Author
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Lavrov, Dennis V., primary and Pett, Walker, additional
- Published
- 2016
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53. Halisarca dujardini
- Author
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Ereskovsky, Alexander V., Lavrov, Dennis V., Boury-Esnault, Nicole, and Vacelet, Jean
- Subjects
Halisarcidae ,Halisarca ,Animalia ,Demospongiae ,Chondrosida ,Biodiversity ,Halisarca dujardini ,Taxonomy ,Porifera - Abstract
Redescription of Halisarca dujardini type species (Figs. 2���23) Previous reviews. L��vi 1956; Bergquist 1996; Bergquist & Cook 2002. Halisarca dujardini Johnston, 1842 Synonymy. Halisarca dujardini Johnston, 1842: 192���193; Lendenfeld 1889: 729���730; de Laubenfels 1948: 175���176; L��vi 1956: 184; Chen 1976: 113���139; Ereskovsky 1993: 8; Bergquist 1996: 24���27; Bergquist & Cook 2002: 1090���1091. Halisarca franz-schulzei Merejkowsky 1878: 27���36, Pl. I, fig. 1���6; Pl. II, fig. 9���15. Hymeniacidon dujardini Bowerbank 1866: 224. Halisarca sputum Topsent 1893: 38 ���39. Original description. Halisarca dujardini, Johnston, 1842, p. 192. Type material. Holotype: presumably lost. Neotype: BMNH 1960.1.7.1���Black Rock, Brighton, English Channel (epizootic on algae, collected close to the type locality) (Bergquist & Cook 2002). Comparative material examined. Sponge specimens used in the revision of Halisarca dujardini were collected using SCUBA, in White Sea (Kandalaksha Bay, Chupa Inlet (66 �� 17 ' 32 "N ��� 33 �� 39 ' 39 "E), 3���5 m depth, from algae Fucus ramosus and Laminaria saccharina, July 2000���2004; in Barents Sea, Kola Peninsula, Dalnije Zelentsi (69 ��07' 19 "N ��� 36 ��03' 21 "E) 0.3���0.5 m depth, July, August 2003; in Bering Sea, Avacha Bay (52 �� 46 ' 32 "N ��� 158 �� 36 ' 16 "E) 10-11 m depth, October 18 2008; in Japan Sea the Gulf of Peter the Great near of the Marine Biological station ���Vostok��� (Marine Biological Institute of Russian Academy of Sciences) (42 �� 54 'N ��� 132 �� 38 'W) from rocks and boulders at a depth 0.4���4 m; in North Sea, Norway, Bergen (60 �� 23 ' 29 "N ��� 5 �� 13 ' 46 "E), June 2009, 6 m depth; in North Sea, Netherlands, Zeeland, Goese Sas (51 �� 38 ' 52 "N ��� 3 �� 48 '0"E) 18 m depth, July, 2009; NE Atlantic, North Wales (53 �� 14 ' 6 "N ��� 4 �� 7 ' 48 "W) July 1988, 3 m. We also investigated histologically a piece of the neotype and a piece of Halisarca franz-schulzei Merejkovsky, 1879 from Zoological Institute RAN, St-Petersburg, Russia. Description. External morphology. Predominantly incrusting sponge, 0.3���12 mm thick, forming smooth crusts on shallow water hard surfaces, or globular, 0.5���2 cm in diameter. Frequently a fouling organism (on red and brown algae, ascidians, shells of bivalves and brachiopods, tubes of sedentary polychaetes, hydroid stalks) (Figs. 2, 3). Incrusting forms have multiple oscula 0.3���1 mm in diameter, scattered regularly; globular sponges have one osculum or, occasionally, two oscula with raised rims, approximately 1���2 mm in diameter. Pores are dispersed. A significant reduction in the aquiferous system is characteristic for the latest phases of reproduction (embryo and larvae development). During these periods oscula and pores are rarely observed. Colour is yellow-beige to pale brown (Fig. 2); during last phases of reproduction the specimens have ivory or whitish colour due to the presence of embryos and larvae (Fig. 3). Surface is smooth and slimy. Consistency is soft, gelatinous and slightly elastic. Anatomy. Soft tissues. An ectosomal region up to 27 ��m thick, consists of three layers: (1) The upper layer composed of a mucous acellular cuticle 0.1���0.2 ��m thick (Figs. 4, 6), underlying external parts of T-shaped exopinacocytes and a diffuse collagen region 0.9���3 ��m thick beneath it; (2) the middle layer ~ 5���10 ��m thick containing interlaced collagen fibrils organized into firm tracts. This layer can include rare spherulous cells; and (3) the inner layer, up to 3���7 ��m thick, consisting of condensed collagen fibrils and the cell bodies of T-shape exopinacocytes. The choanosome makes up the greatest volume of the sponge body and is composed of choanocyte chambers, canals and mesohyl (Fig. 4). The organization of the aquiferous system is reminiscent of a syconoid system described earlier (L��vi 1956; Vacelet et al. 1989). The long, branching, tubular, meandering choanocyte chambers are arranged radially around a large exhalant canal (Fig. 4). Choanocyte chambers could vary in abundance and size depending on life cycle. During active growth period choanocyte chambers are 120���600 ��m long and 24���90 ��m in diameter. Abundance and length of choanocyte chambers decrease during reproduction (Fig. 5). Cytology. Choanocytes (Figs. 7, 8) are cylindrical or trapeziform, with long and numerous basal pseudopods (Vacelet et al. 1989; Boury-Esnault et al. 1990; Gonobobleva & Maldonado 2009). The cells are 6���9.5 ��m long and 3.5���5 ��m wide, with a smooth flagellum and a collar composed of 30���40 microvilli. Some but not all cells have a periflagellar asymmetrical cytoplasmic sleeve. Choanocytes within a choanocyte chamber are connected with each other at the basal-lateral surfaces with numerous interdigitations. Nuclei are pyriform (2.5 x 4.8 ��m) with apical thinning and often with one to three nucleoli. Cytoplasm contains phagosomes, electron transparent vacuoles, perinuclear Golgi complexes, and mitochondria. Exopinacocytes (Figs. 9���11) are T-shaped. External flat cytoplasmic parts connect with each other by interdigitations. Cell bodies, including the nucleus and the main cytoplasm volume, are situated beneath the ectosome. Cell bodies are connected with flat cytoplasmic parts by thin and long cytoplasmic bridges. Nuclei are nucleolated. Endopinacocytes (Figs. 12, 13) are flat fusiform or polygonal in shape. A nucleolated nucleus is oval, 1.6��� 2 x 3���3.8 ��m in size, and is located in the center of the cell. The cytoplasm includes well-developed Golgi complexes, small electron dense spherical inclusions and abundant electron-transparent vacuoles. Basopinacocytes (Figs. 14, 15) are flattened and polygonal, about 8���14 ��m in length and about 2 ��m in width. The cytoplasm includes a well-developed Golgi complex, small electron dense spherical inclusions and some phagosomes. Mesohylar cells. L��vi (1956) was the first to describe the free cells in the mesohyl of H. dujardini at light microscopy level. He distinguished three cells populations (types): (1) amoeboid or star-shaped cells with spherical central nucleus and clear cytoplasm containing small granules, called ���amoebocytes I and II���, or amoebocytes and collencytes; (2) the cells with the cytoplasm filled with acidophilic granules, called ���amoebocytes III���, or fuchsinophil cells, or granular cells; and (3) cells with large peripheral nucleus and the cytoplasm filled with big spherical inclusions ��� spherulous cells. In subsequent works (Bergquist 1996; Bergquist & Cook 2002) three types of mesohylar cells were also mentioned: (1) lophocytes; (2) spherulous cells, common in the zone between ectosome and choanosome and along canals; and (3) fuchsinophilic cells scattered throughout the choanosome. However, the use of electron microscopy led to recognition of six mesohylar cells types in H. dujardini: (1) amoebocytes, (2) collencytes or lophocytes, (3) spherulous cells, (4) granular cells, (5) microgranular cells, and (6) vacuolar cells (Volkova & Zolotareva 1981; Korotkova & Ermolina 1986; Sukhodolskaya & Krasukevitch, 1984), which are described below. (1) Archaeocytes (���amoebocytes I���) (Figs. 16, 17) are abundant cells in H. dujardini mesohyl. These cells have an irregular amoeboid shape and often produce pseudopodia. A large spherical nucleolated nucleus (2.5���3.5 ��m in diameter) is located in the center of the cell. Cytoplasm is characterized by the absence of any special or monotypical inclusions, although it can contain heterophagosomes and various osmiophilic or electron-transparent inclusions. There are well developed Golgi complex and endoplasmic reticulum. Archaeocytes are distributed throughout the mesohyl. (2) Lophocytes (Figs. 18, 19) have a star-like, clavate, or oval form, often with a tuft of secreted collagen fibrils attached to the lateral and posterior ends. The cytoplasm contains some phagosomes and small osmiophilic inclusions. An oval nucleolated nucleus is located in the anterior part of the cell. (3) Spherulous cells (Fig. 20) are oval or round in appearance (8���12 ��m in diameter) and are characterized by the presence in the cytoplasm of 2���7 large trapeziform, spherical, or oval homogenous osmiophilic inclusions 2���8 ��m in diameter. These inclusions have a microgranular structure. The cytosol is reduced to a thin layer between these inclusions. The cytoplasm sometimes contains large heterogenous inclusions and small electron transparent vacuoles. The Golgi complex is well developed. A nucleus without nucleoli could be in the cell���s center or at the periphery. Spherulous cells can be distributed anywhere in the mesohyl, but are more common in external parts of the choanosome. They often occupy the collagen-reinforced layer in the sponge ectosome. (4) Granular cells (amoebocytes III or fuchsinophilic cells) (Fig. 20) form one of the more numerous cell types in the mesohyl. The shape of these cells is highly variable; usually cells are irregular, ovoid or elongate with a mean diameter about 8 ��m. The cytoplasm is filed with round or oval electron-dense homogenous granules (0.5��� 2 ��m in diameter). The nucleus has a peripheral, or, rarely, central location in the cell. The cells are distributed throughout the choanosome. (5) Microgranular cells (Fig. 20). We propose to distinguish this cell type in H. dujardini from granular cells. Microgranular cells are characterized by irregular, amoeboid or, rarely, oval shape and have large lobopodia. The cytoplasm is filed with abundant small (0.2���0.5 ��m in diameter) electron-dense spherical or oval inclusions. These inclusions can be of oval shape or rod-shaped. The Golgi complex is well developed. The nucleus can be nucleolated or without nucleoli, located in the cell���s center or at the periphery. Microgranular cells do not display any special localization in the choanosome. (6) Vacuolar cells (Fig. 20) are rare in the mesohyl of H. dujardini but do not represent a stage in the ontogenesis of spherulous cell, as thought by L��vi (1956). Cells are irregular to oval in shape, 5 x 7���9 x 12 ��m in size. The cytoplasm contains one to 12 vacuoles of oval or elongated shape 0.5���7.2 ��m in diameter. Vacuoles are electrontransparent or could contain very loose mucus-like inclusions, and in sometimes intact symbiotic bacteria. Vacuolar cells are predominantly distributed in the middle part of the choanosome. Additional transient mesohylar cell types could differentiate at various stages in the life cycle. They can be nutritive cells, macrophages, and special granular cells containing cationic peptides and proteins. Nutritive cells (Fig. 21) are a mixed heterogeneous cell population with predominance of dedifferentiated choanocytes. Choanocytes filled with phagosomes leave choanocyte chambers and enter the mesohyl during oocytes vitellogenesis (Korotkova & Apalkova 1975; Korotkova & Aisenshtadt 1976; Aisenshtadt & Korotkova 1976). Among the nutritive cells there are also amoebocytes I and spherulous cells. Nutritive cells are phagocyted by growing oocytes for yolk granules formation. Macrophages (Fig. 22) are large cells that appear at the end of sexual reproduction when begins the postreproductive restoration phase of the life cycle (Ereskovsky 2000), or during the regeneration when it undergoes destructive processes in the mesohyl (Korotkova & Movchan 1973; Volkova & Zolotareva 1981; Korotkova & Ermolina 1986 b; Sukhodolskaya & Krasukevitch 1984). Cell dimensions can reach 30���35 ��m, the cytoplasm is filled with large heterogeneous phagosomes. A large spherical nucleus is nucleolated. Special eosinophilic granular cells (Fig. 23) contain cationic peptides and proteins (Krylova et al. 2004). These cells are amoeboid or oval in shape (about 8���12 ��m in diameter); the nucleus is oval and voluminous (about 3.2 ��m in diameter) with condensed heterochromatin or a small nucleolus. The cytoplasm contains several specific inclusions: (1) vacuoles that include one to ten round or oval electron-dense granules with peripheral thinly-fibrillar material; (2) vacuoles with electron-dense fine-granular inclusions; (3) electron-dense thinly-fibrillar inclusions located in the cytoplasm. Cells differentiate at the beginning of vitellogenesis of oocytes. During the embryonic development they concentrate in the mesohyl surrounding embryos. These eosinophilic granular cells (or eosinophilic amoebocytes) of maternal sponge penetrate developing embryos and remain there until the beginning of metamorphosis (Korotkova & Ermolina 1982; Ereskovsky & Gonobobleva 2000; Gonobobleva & Ereskovsky 2004 a, b). Symbiotic bacteria. Symbiotic bacteria of H. dujardini are represented by a single morphotype found both in the mesohyl of all investigated adults (Fig. 20) and during all stages of embryonic development of the White Sea specimens (Ereskovsky et al. 2005). Bacteria are almost evenly distributed in the mesohyl and do not form accumulations. Sometimes bacteria are located in vacuoles of archaeocytes. Bacteria (likely gram-positive) have a curved spiral form, characteristic of spirills (Fig. 20). Their length is about 0.45 ��m, thickness 0.18 ��m, the cell wall is 0.05 ��m thick. No flagella or piles are found at the surface of bacterial wall. The cytoplasm is heterogeneous. Its peripheral part has a medium electronic density, while the central part is electron dense and possibly corresponds to the nucleoid. In-between, a thin electron-transparent layer is visible. Reproduction. The sponge is dioecious (however some rare individuals could be hermaphrodites) with short seasonal period of reproduction (Table 2). Spermatogenesis occurs only during the cold part of the year (Ereskovsky 2000). Larvae are sub-spherical to oval dispherulae, 100���200 ��m in diameter, completely ciliated but only sparsely so at the posterior pole (Ereskovsky & Gonobobleva 2000; Gonobobleva & Ereskovsky 2004 a, b). Habitat. Halisarca dujardini is usually found at depths from 1 to 20 m but also from upper littoral (Barents Sea) to 300 m (Skagerrak), mainly on the algae Fucus vesiculosus, F. serratus, Ascophyllum nodosum and Laminaria saccharina, under and on stones and boulders, in empty shells of lamellibranchs, on carapaces of crabs, at the base of gorgonians, and on the ascidian Styela rustica. Distribution. Halisarca dujardini species complex is considered to be cosmopolitan (Bergquist & Cook 2002). In fact, however, its distribution is limited to temperate waters: in the North Atlantic���along the European costs from English Channel to White Sea and in Atlantic coast of USA (Massachusetts) and in the North-West of Mediterranean Sea; in North Pacific���Bering Sea, Avacha Bay and in Russian coast of Japan Sea; in South Pacific���the New Zealand coasts (Fig. 24). See Annex 1 for the detailed distribution. Material examined. Holotype: collected in ���Grotte �� Corail��� Maire Island, 16 m depth, 43 �� 12 ' 38.04 "N ��� 5 �� 19 ' 56.80 "E, Mus��um National d'Histoire Naturelle (Paris, France) MNHN DJV 128. Paratype: collected in ���Grotte �� Corail��� Maire Island, 16 m depth, 43 �� 12 ' 38.04 "N ��� 5 �� 19 ' 56.80 "E, Zoological Institute RAS (Saint-Petersburg, Russia) № 11141. Description. External morphology. Thinly incrusting sponge, 0.17���0.19 mm thick, spreading on the surface of the living bryozoan Smittina cervicornis (Fig. 25, 26). The sponge covers the host���s colony from the base to the tips of the branches with a continuous layer. Most often, the sponge coating is very thin and transparent, and thus hardly visible. The sponge may become relatively thick and then appears as an opaque sheath. The surface is skinlike, lustreless and smooth, even (Fig. 26). Oscula have a cone shape (height: 0.1���0.5 ��m and diameter about 0.5 mm) and are located exclusively along the bryozoan branch edges that are devoid of zooid orifices. Texture is soft, very delicate and easily torn. The colour is pale-yellow. Internal organization. Soft tissue organization. There is a thin ectosomal region, 4���14 ��m deep, consisting of the flat part of exopinacocytes and of an underlying dense collagen layer, about 1.7���2.6 ��m deep (Fig. 27). This layer contains symbiotic bacteria and some secretory cells (Fig. 27). Cell bodies of T-shape exopinacocytes and rare spherulous cells occur beneath the collagen layer. The choanosome makes up most of the volume of the sponge body and is composed of choanocyte chambers and mesohyl (Figs. 27, 28). The individual choanocyte chambers are tubular in shape, sometimes branched, measuring from 76 up to 175 ��m in length and are 9.3���14 ��m wide. There are mobile cells present in the mesohyl. The basal part (Fig. 29), in contact with the bryozoan surface, includes a dense, thin (0.17 ��m) cuticle secreted by the basopinacocytes. Collagen cuticle includes spiral symbiotic bacteria and other bacteria, which are not present in other sponge parts. Cytology. Exopinacocytes (Fig. 30) are T-shaped with a thin, flattened external cytoplasmic part, and an internal cell body. The cell body is irregular or triangular in shape, about 4.9 x 5.3 ��m. The two parts of the cell are connected by a thin cytoplasmic bridge. Nucleus is lightly ovoid (2.2���2.4 ��m in diameter), often without nucleolus. Choanocytes (Fig. 28, 31) are elongate or roughly pyramidal, 2.3���5.3 ��m wide at the base and 1.9���4.2 ��m wide at the nucleus area, the height is 4���5.9 ��m. Choanocyte collar arises at approximately 4 / 5 of the height of the cell and is composed of about 18 microvilli. Nucleus is central or apical, spherical about 1.9 ��m in diameter, occasionally with a nucleolus, 0.5 ��m in diameter. The apical part of choanocytes encompasses many small vacuoles. The central and basal cytoplasm usually contains 2���4 phagosomes, 0.8���1.5 ��m in diameter with heterogeneous inclusions. The choanocytes also contain mitochondria, osmiophilic granules (0.3���0.6 ��m), electron transparent vacuoles (0.1���0.8 ��m) and other inclusions. The choanocytes contact each other only at the base. Long fine pseudopodia frequently arise from the central and basal parts of the choanocytes; the latter anchor choanocytes in the mesohyl. The free apical surface of the choanocytes and the flagella are covered by a thin (1 ��m) glycocalyx layer. Endopinacocytes (Fig. 32), Published as part of Ereskovsky, Alexander V., Lavrov, Dennis V., Boury-Esnault, Nicole & Vacelet, Jean, 2011, Molecular and morphological description of a new species of Halisarca (Demospongiae: Halisarcida) from Mediterranean Sea and a redescription of the type species Halisarca dujardini, pp. 5-31 in Zootaxa 2768 on pages 10-25, DOI: 10.5281/zenodo.206842, {"references":["Levi, C. (1956) Etude des Halisarca de Roscoff. Embryologie et systematique des demosponges. Archives de Zoologie experimentale et generale, 93, 1 - 184.","Bergquist, P. R. (1996) The marine fauna of New Zealand. Porifera, Class Demospongiae. Part 5: Dendroceratida & Halisarcida. Memoirs of the New Zealand Oceanographic Institute, 107, 1 - 53.","Bergquist, P. R. & Cook, S. C. (2002) Order Halisarcida Bergquist, 1996. In: Hooper, J. N. A. & Soest van, R. W. M. (Eds.), Systema Porifera: A guide to the classification of sponges, Kluwer Academic / Plenum Publishers, New York, pp. 1089.","Johnston, G. (1842) A history of British sponges and lithophytes. Lizard, WH, Edinburgh, 264 pp.","Lendenfeld, R. von (1889) A monograph of the Horny Sponges. Trubner and Co, Ludgate Hill, EC, London, 936 pp.","Laubenfels, M. W. de (1948) The order Keratosa of the phylum Porifera. A monographic study. Allan Hancock Foundation Publications Occasional Paper, 3, 1 - 217.","Chen, W. T. (1976) Reproduction and speciation in Halisarca. In: Harrison, F. W. & Cowden, R. R. (Eds.), Aspects of sponge biology, Academic Press, New York, pp. 113 - 140.","Ereskovsky, A. V. (1993) Addition to the fauna of sponges (Porifera) of the White Sea. Vestnik of St-Petersburg University, 2, 3 - 12.","Merejkowsky, C. D. (1878) Les eponges de la mer Blanche. Memoires de l'Academie imperiales des Sciences de St Petersbourg, 26, 1 - 51.","Bowerbank, J. S. (1866) A monograph of the British Spongiadae. Robert Hardwicke, London, 388 pp.","Topsent, E. (1893) Nouvelle serie de diagnoses d'eponges de Roscoff et de Banyuls Archives de Zoologie experimentale et generale, 1, 33 - 43.","Vacelet, J., Boury-Esnault, N., De Vos, L. & Donadey, C. (1989) Comparative study of the choanosome of Porifera: II. The Keratose Sponges. Journal of Morphology, 201, 119 - 129.","Boury-Esnault, N., De Vos, L., Donadey, C. & Vacelet, J. (1990) Ultrastructure of choanosome and sponge classification. In: Rutzler, K. (Ed.), New Perspectives in Sponge Biology, Smithsonian Institution Press, Washington, pp. 237 - 244.","Gonobobleva, E. L. & Maldonado, M. (2009) Choanocyte ultrastructure in Halisarca dujardini (Demospongiae, Halisarcida).","Volkova, M. A. & Zolotareva, G. A. (1981) The development of Halisarca dujardini Johnston from conglomerates of somatic cells. In: Korotkova, G. P., (Ed.), Morphogenesis in sponges, Leningrad University Press, Leningrad, pp. 74 - 92.","Sukhodolskaya, A. N. & Krasukevitch, T. N. (1984) The effect of inozine on the development of Halisarca dujardini from small fragments of the body. Vestnik of Leningrad University, 3, 56 - 62.","Korotkova, G. P. & Apalkova, L. V. (1975) Oogenesis of the Barents Sea sponge Halisarca dujardini Johnston. In: Tokin, B. P., (Ed.), Comparative and experimental morphology of the sea organisms, Kola Filial Academy of Sciences USSR Press, Murmansk, pp. 9 - 26.","Korotkova, G. P. & Movchan N. A. (1973) The peculiarities of defensive-regenerational processes of the sponge Halisarca dujardini. Vestnik Leningradskogo Universiteta, 21, 16 - 25.","Korotkova, G. P. & Ermolina, N. O. (1986 b) Destruction of embryos during the reproductive period in the White Sea sponge Halisarca dujardini Johnston (Demospongiae). Vestnik Leningradskogo Universiteta (Biologia), 4, 104 - 106.","Krylova, D. D., Aleshina, G. M., Kokryakov, V. N. & Ereskovsky, A. V. (2004) Antimicrobal propeties of mesohylar granular cells of Halisarca dujardini Johnston, 1842 Demospongiae, Halisarcida). In: Pansini, M., Pronzato, R., Bavestrello, G., & Manconi, R., (Eds.), Sponge science in the new millennium. Bollettino dei Musei e degli Instituti Biologici dell' Universita di Genova, 68, pp. 399 - 404.","Korotkova, G. P. & Ermolina, N. O. (1982) The larval development of Halisarca dujardini (Demospongiae). Zoological Journal, 61, 1472 - 1480.","Ereskovsky, A. V. & Gonobobleva, E. L. (2000) New data on embryonic development of Halisarca dujardini Johnston, 1842 (Demospongiae, Halisarcida). Zoosystema, 22, 355 - 368.","Gonobobleva, E. L. & Ereskovsky, A. V. (2004 a) Metamorphosis of the larva of Halisarca dujardini (Demospongiae, Halisarcida). Bulletin de l'Institut royal des Sciences naturelles de Belgique, Biologie, 74, 101 - 115.","Gonobobleva, E. L. & Ereskovsky, A. V. (2004 b) Polymorphism in free-swimming larvae of Halisarca dujardini (Demospongiae, Halisarcida). In: Pansini, M., Pronzato, R., Bavestrello, G. & Manconi, R., (Eds.), Sponge science in the new millennium. Bollettino dei Musei e degli Instituti Biologici dell' Universita di Genova, 68, pp. 349 - 356.","Ereskovsky, A. V., Gonobobleva, E. L. & Vishnyakov, A. E. (2005) Morphological evidence for vertical transmission of symbiotic bacteria in the viviparous sponge Halisarca dujardini Johnston (Porifera, Demospongiae, Halisarcida). Marine Biology, 146, 869 - 875.","Duran, S. & Rutzler, K. (2006) Ecological speciation in a Caribbean marine sponge. Molecular Phylogenetics and Evolution, 40, 292 - 297.","Lavrov, D. V. (2010) Rapid proliferation of repetitive palindromic elements in mtDNA of the endemic baikalian sponge Lubomirskia baicalensis. Molecular Phylogeneny and Evolution, 27, 757 - 760.","Lavrov, D. V., Wang, X. & Kelly, M. (2008) Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data. Molecular Phylogeneny and Evolution, 49, 111 - 124."]}
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- 2011
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54. Bajalus Lendenfeld 1885
- Author
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Ereskovsky, Alexander V., Lavrov, Dennis V., Boury-Esnault, Nicole, and Vacelet, Jean
- Subjects
Halisarcidae ,Animalia ,Demospongiae ,Biodiversity ,Bajalus ,Chondrillida ,Taxonomy ,Porifera - Abstract
Bajalus Lendenfeld, 1885 Diagnosis. Halisarcida in which the choanocyte chambers are tubular, branched, and wide mouthed. Larvae are incubated dispherulae (a larval form found only in Halisarca) with simple undifferentiated histology and cilia of uniform length. Skeleton is composed of fibrillar collagen only, there are no fibrous or mineral elements present; ectosomal and subectosomal collagen is highly organised and structurally diversified (modified from Bergquist & Cook 2002). Type species: Halisarca dujardini Johnston, 1842: 192., Published as part of Ereskovsky, Alexander V., Lavrov, Dennis V., Boury-Esnault, Nicole & Vacelet, Jean, 2011, Molecular and morphological description of a new species of Halisarca (Demospongiae: Halisarcida) from Mediterranean Sea and a redescription of the type species Halisarca dujardini, pp. 5-31 in Zootaxa 2768 on page 10, DOI: 10.5281/zenodo.206842, {"references":["Bergquist, P. R. & Cook, S. C. (2002) Order Halisarcida Bergquist, 1996. In: Hooper, J. N. A. & Soest van, R. W. M. (Eds.), Systema Porifera: A guide to the classification of sponges, Kluwer Academic / Plenum Publishers, New York, pp. 1089.","Johnston, G. (1842) A history of British sponges and lithophytes. Lizard, WH, Edinburgh, 264 pp."]}
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- 2011
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55. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple
- Author
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Ismail, Siti Izera, Batzer, Jean Carlson, Harrington, Thomas C., Crous, Pedro W., Lavrov, Dennis V., Li, Huanyu, Gleason, Mark L., Ismail, Siti Izera, Batzer, Jean Carlson, Harrington, Thomas C., Crous, Pedro W., Lavrov, Dennis V., Li, Huanyu, and Gleason, Mark L.
- Abstract
Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi.
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- 2015
56. Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism
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Pett, Walker, primary and Lavrov, Dennis V., additional
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- 2015
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57. Systematics and Molecular Phylogeny of the Family Oscarellidae (Homoscleromorpha) with Description of Two New Oscarella Species
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Gazave, Eve, Lavrov, Dennis V., Cabrol, Jory, Renard, Emmanuelle, Rocher, Caroline, Vacelet, Jean, Adamska, Maja, Borchiellini, Carole, Ereskovsky, Alexander V., Gazave, Eve, Lavrov, Dennis V., Cabrol, Jory, Renard, Emmanuelle, Rocher, Caroline, Vacelet, Jean, Adamska, Maja, Borchiellini, Carole, and Ereskovsky, Alexander V.
- Abstract
The family Oscarellidae is one of the two families in the class Homoscleromorpha (phylum Porifera) and is characterized by the absence of a skeleton and the presence of a specific mitochondrial gene, tatC. This family currently encompasses sponges in two genera: Oscarella with 17 described species and Pseudocorticium with one described species. Although sponges in this group are relatively well-studied, phylogenetic relationships among members of Oscarellidae and the validity of genus Pseudocorticium remain open questions. Here we present a phylogenetic analysis of Oscarellidae using four markers (18S rDNA, 28S rDNA, atp6, tatC), and argue that it should become a mono-generic family, with Pseudocorticium being synonymized with Oscarella, and with the transfer of Pseudocorticium jarrei to Oscarella jarrei. We show that the genus Oscarella can be subdivided into four clades, each of which is supported by either a small number of morphological characters or by molecular synapomorphies. In addition, we describe two new species of Oscarella from Norwegian fjords: O. bergenensis sp. nov. and O. nicolae sp. nov., and we compare their morphology, anatomy, and cytology with other species in this genus. Internal anatomical characters are similar in both species, but details of external morphology and particularly of cytological characters provide diagnostic features. Our study also confirms that O. lobularis and O. tuberculata are two distinct polychromic sibling species. This study highlights the difficulties of species identification in skeleton-less sponges and, more generally, in groups where morphological characters are scarce. Adopting a multi-marker approach is thus highly suitable for these groups.
- Published
- 2013
- Full Text
- View/download PDF
58. Eight new mtDNA sequences of glass sponges reveal an extensive usage of +1 frameshifting in mitochondrial translation
- Author
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Haen, Karri M., primary, Pett, Walker, additional, and Lavrov, Dennis V., additional
- Published
- 2014
- Full Text
- View/download PDF
59. Systematics and Molecular Phylogeny of the Family Oscarellidae (Homoscleromorpha) with Description of Two New Oscarella Species
- Author
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Gazave, Eve, primary, Lavrov, Dennis V., additional, Cabrol, Jory, additional, Renard, Emmanuelle, additional, Rocher, Caroline, additional, Vacelet, Jean, additional, Adamska, Maja, additional, Borchiellini, Carole, additional, and Ereskovsky, Alexander V., additional
- Published
- 2013
- Full Text
- View/download PDF
60. Five new species of Homoscleromorpha (Porifera) from the Caribbean Sea and re-description ofPlakina jamaicensis
- Author
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Ereskovsky, Alexander V., primary, Lavrov, Dennis V., additional, and Willenz, Philippe, additional
- Published
- 2013
- Full Text
- View/download PDF
61. AnimalMitochondrial DNA asWe Do Not Know It:mt-Genome Organization and Evolution in Nonbilaterian Lineages.
- Author
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Lavrov, Dennis V. and Pett, Walker
- Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0–25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitutionrates,andalargerangeofgenomesizes.Thisnewlydiscovereddiversityallowsabetterunderstandingoftheevolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
62. Cnidarian phylogenetic relationships as revealed by mitogenomics
- Author
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Kayal, Ehsan, primary, Roure, Béatrice, additional, Philippe, Hervé, additional, Collins, Allen G, additional, and Lavrov, Dennis V, additional
- Published
- 2013
- Full Text
- View/download PDF
63. Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): Six Linear Chromosomes, Fragmented rRNAs, tRNA Editing, and a Novel Genetic Code
- Author
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Lavrov, Dennis V., primary, Pett, Walker, additional, Voigt, Oliver, additional, Wörheide, Gert, additional, Forget, Lise, additional, Lang, B. Franz, additional, and Kayal, Ehsan, additional
- Published
- 2012
- Full Text
- View/download PDF
64. Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians
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Kayal, Ehsan, primary, Bentlage, Bastian, additional, Collins, Allen G., additional, Kayal, Mohsen, additional, Pirro, Stacy, additional, and Lavrov, Dennis V., additional
- Published
- 2011
- Full Text
- View/download PDF
65. Extreme mitochondrial evolution in the ctenophoreMnemiopsis leidyi: Insight from mtDNA and the nuclear genome
- Author
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Pett, Walker, primary, Ryan, Joseph F., additional, Pang, Kevin, additional, Mullikin, James C., additional, Martindale, Mark Q., additional, Baxevanis, Andreas D., additional, and Lavrov, Dennis V., additional
- Published
- 2011
- Full Text
- View/download PDF
66. RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleriby ingested dsRNA expressing bacteria
- Author
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Rivera, Ajna S, primary, Hammel, Jörg U, additional, Haen, Karri M, additional, Danka, Elizabeth S, additional, Cieniewicz, Brandon, additional, Winters, Ian P, additional, Posfai, Dora, additional, Wörheide, Gert, additional, Lavrov, Dennis V, additional, Knight, Scott W, additional, Hill, Malcolm S, additional, Hill, April L, additional, and Nickel, Michael, additional
- Published
- 2011
- Full Text
- View/download PDF
67. Gene recruitment – A common mechanism in the evolution of transfer RNA gene families
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Wang, Xiujuan, primary and Lavrov, Dennis V., additional
- Published
- 2011
- Full Text
- View/download PDF
68. Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
- Author
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Philippe, Hervé, primary, Brinkmann, Henner, additional, Lavrov, Dennis V., additional, Littlewood, D. Timothy J., additional, Manuel, Michael, additional, Wörheide, Gert, additional, and Baurain, Denis, additional
- Published
- 2011
- Full Text
- View/download PDF
69. Molecular and morphological description of a new species of Halisarca (Demospongiae: Halisarcida) from Mediterranean Sea and a redescription of the type species Halisarca dujardini
- Author
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ERESKOVSKY, ALEXANDER V., primary, LAVROV, DENNIS V., additional, BOURY-ESNAULT, NICOLE, additional, and VACELET, JEAN, additional
- Published
- 2011
- Full Text
- View/download PDF
70. Molecular Phylogeny Restores the Supra-Generic Subdivision of Homoscleromorph Sponges (Porifera, Homoscleromorpha)
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Gazave, Eve, primary, Lapébie, Pascal, additional, Renard, Emmanuelle, additional, Vacelet, Jean, additional, Rocher, Caroline, additional, Ereskovsky, Alexander V., additional, Lavrov, Dennis V., additional, and Borchiellini, Carole, additional
- Published
- 2010
- Full Text
- View/download PDF
71. Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda
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Rota-Stabelli, Omar, primary, Kayal, Ehsan, additional, Gleeson, Dianne, additional, Daub, Jennifer, additional, Boore, Jeffrey L., additional, Telford, Maximilian J., additional, Pisani, Davide, additional, Blaxter, Mark, additional, and Lavrov, Dennis V., additional
- Published
- 2010
- Full Text
- View/download PDF
72. Rapid Proliferation of Repetitive Palindromic Elements in mtDNA of the Endemic Baikalian Sponge Lubomirskia baicalensis
- Author
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Lavrov, Dennis V., primary
- Published
- 2009
- Full Text
- View/download PDF
73. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications
- Author
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Wang, Xiujuan, primary, Huang, Yong, additional, Lavrov, Dennis V, additional, and Gu, Xun, additional
- Published
- 2009
- Full Text
- View/download PDF
74. The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE)
- Author
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Erpenbeck, Dirk, primary, Voigt, Oliver, additional, Wörheide, Gert, additional, and Lavrov, Dennis V, additional
- Published
- 2009
- Full Text
- View/download PDF
75. Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae
- Author
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Wang, Xiujuan, primary and Lavrov, Dennis V., additional
- Published
- 2008
- Full Text
- View/download PDF
76. The mitochondrial genome of Hydra oligactis (Cnidaria, Hydrozoa) sheds new light on animal mtDNA evolution and cnidarian phylogeny
- Author
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Kayal, Ehsan, primary and Lavrov, Dennis V., additional
- Published
- 2008
- Full Text
- View/download PDF
77. Sequencing complete mitochondrial and plastid genomes
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Burger, Gertraud, primary, Lavrov, Dennis V, additional, Forget, Lise, additional, and Lang, B Franz, additional
- Published
- 2007
- Full Text
- View/download PDF
78. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase
- Author
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Shao, Zhiyong, primary, Graf, Shannon, additional, Chaga, Oleg Y., additional, and Lavrov, Dennis V., additional
- Published
- 2006
- Full Text
- View/download PDF
79. Complete mtDNA Sequences of Two Millipedes Suggest a New Model for Mitochondrial Gene Rearrangements: Duplication and Nonrandom Loss
- Author
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Lavrov, Dennis V., primary, Boore, Jeffrey L., additional, and Brown, Wesley M., additional
- Published
- 2002
- Full Text
- View/download PDF
80. Five new species of Homoscleromorpha (Porifera) from the Caribbean Sea and re-description of Plakina jamaicensis.
- Author
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Ereskovsky, Alexander V., Lavrov, Dennis V., and Willenz, Philippe
- Abstract
Five new species of Homoscleromorpha (Porifera) of four genera, Oscarella, Plakortis, Plakina and Corticium, are described from vertical walls of reef caves at depths ranging from 23 to 28 m in the Caribbean Sea. Oscarella nathaliae sp. nov. has a leaf-like thinly encrusting, flat body, loosely attached to the substrate and a perforated, not lobate surface. Oscarella nathaliae sp. nov. contains two bacterial morphotypes and is characterized by two mesohylar cell types with inclusions. Plakortis myrae sp. nov. has diods of two categories: abundant large ones (83–119 μm long) and rare small ones (67–71 μm long) with sinuous, S-bent centres; triods Y- or T-shaped (18–5 μm long), and abundant microrhabds (5–12 μm long). Plakortis edwardsi sp. nov. has diods of one category with thick, sinuous, S-bent centres (110 to 128 μm long); triods T-shaped (actines 28–59 μm long). It is the only species of this genus showing small diods (22–31 μm long). Plakortis dariae sp. nov. has diods of two categories: large ones (67–112 μm long) and small, rare, irregular ones, slightly curved, often deformed with one end blunt (30–59 μm long); triods rare and regular (actines 20–44 μm long). Corticium diamantense sp. nov. has oscula situated near its border, regular non-lophose calthrops of one size-class, very rare tetralophose calthrops and candelabra with the fourth actine ramified basally in 4–5 microspined rays. In addition, a re-description of Plakina jamaicensis is based on newly collected material and the type specimen. Plakortis jamaicensis has a convoluted brain-like surface; well developed sub-ectosomal cavities; irregular sinuous diods, triods, calthrops, rare monolophose calthrops, rare dilophose calthrops, rare trilophose calthrops and common tetralophose calthrops. Molecular ‘barcoding’ sequences for mitochondrial cob are given for Plakortis edwardsi sp. nov., P. dariae sp. nov., Plakina jamaicensis and Corticium diamantense sp. nov. An identification key for all western Atlantic Homoscleromorpha is provided. [ABSTRACT FROM PUBLISHER]
- Published
- 2014
- Full Text
- View/download PDF
81. Systematics and Molecular Phylogeny of the Family Oscarellidae (Homoscleromorpha) with Description of Two New Oscarella Species
- Author
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Gazave, Eve, Lavrov, Dennis V., Cabrol, Jory, Renard, Emmanuelle, Rocher, Caroline, Vacelet, Jean, Adamska, Maja, Borchiellini, Carole, and Ereskovsky, Alexander V.
- Subjects
- *
SPONGES (Invertebrates) , *MOLECULAR phylogeny , *MITOCHONDRIAL DNA , *MARINE ecology , *ANIMAL species , *GENETIC markers , *ANIMAL classification - Abstract
The family Oscarellidae is one of the two families in the class Homoscleromorpha (phylum Porifera) and is characterized by the absence of a skeleton and the presence of a specific mitochondrial gene, tatC. This family currently encompasses sponges in two genera: Oscarella with 17 described species and Pseudocorticium with one described species. Although sponges in this group are relatively well-studied, phylogenetic relationships among members of Oscarellidae and the validity of genus Pseudocorticium remain open questions. Here we present a phylogenetic analysis of Oscarellidae using four markers (18S rDNA, 28S rDNA, atp6, tatC), and argue that it should become a mono-generic family, with Pseudocorticium being synonymized with Oscarella, and with the transfer of Pseudocorticium jarrei to Oscarella jarrei. We show that the genus Oscarella can be subdivided into four clades, each of which is supported by either a small number of morphological characters or by molecular synapomorphies. In addition, we describe two new species of Oscarella from Norwegian fjords: O. bergenensis sp. nov. and O. nicolae sp. nov., and we compare their morphology, anatomy, and cytology with other species in this genus. Internal anatomical characters are similar in both species, but details of external morphology and particularly of cytological characters provide diagnostic features. Our study also confirms that O. lobularis and O. tuberculata are two distinct polychromic sibling species. This study highlights the difficulties of species identification in skeleton-less sponges and, more generally, in groups where morphological characters are scarce. Adopting a multi-marker approach is thus highly suitable for these groups. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
82. Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians.
- Author
-
Kayal, Ehsan, Bentlage, Bastian, Collins, Allen G., Kayal, Mohsen, Pirro, Stacy, and Lavrov, Dennis V.
- Subjects
MITOCHONDRIAL DNA ,JELLYFISHES ,GENE expression ,DNA replication ,GENETICS ,BIOLOGICAL evolution - Abstract
In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
83. Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges
- Author
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Lavrov, Dennis V., Maikova, Olga O., Pett, Walker, and Belikov, Sergey I.
- Subjects
- *
SPONGES (Invertebrates) , *GENOMES , *DEMOSPONGIAE , *MITOCHONDRIAL DNA , *TRANSFER RNA , *PHYLOGENY - Abstract
Abstract: Demosponges, the largest and most diverse class in the phylum Porifera, possess mitochondrial DNA (mtDNA) markedly different from that in other animals. Although several studies investigated evolution of demosponge mtDNA among major lineages of the group, the changes within these groups remain largely unexplored. Recently we determined mitochondrial genomic sequence of the Lake Baikal sponge Lubomirskia baicalensis and described proliferation of small inverted repeats (hairpins) that occurred in it since the divergence between L. baicalensis and the most closely related cosmopolitan freshwater sponge Ephydatia muelleri. Here we report mitochondrial genomes of three additional species of Lake Baikal sponges: Swartschewskia papyracea, Rezinkovia echinata and Baikalospongia intermedia morpha profundalis (Demospongiae, Haplosclerida, Lubomirskiidae) and from a more distantly related freshwater sponge Corvomeyenia sp. (Demospongiae, Haplosclerida, Metaniidae). We use these additional sequences to explore mtDNA evolution in Baikalian sponges, paying particular attention to the variation in the rates of nucleotide substitutions and the distribution of hairpins, abundant in these genomes. We show that most of the changes in Lubomirskiidae mitochondrial genomes are due to insertion/deletion/duplication of these elements rather than single nucleotide substitutions. Thus inverted repeats can act as an important force in evolution of mitochondrial genome architecture and be a valuable marker for population- and species-level studies in this group. In addition, we infer (((Rezinkovia+Lubomirskia)+Swartschewskia)+Baikalospongia) phylogeny for the family Lubomirskiidae based on the analysis of mitochondrial coding sequences from freshwater sponges. [Copyright &y& Elsevier]
- Published
- 2012
- Full Text
- View/download PDF
84. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome.
- Author
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Pett, Walker, Ryan, Joseph F., Pang, Kevin, Mullikin, James C., Martindale, Mark Q., Baxevanis, Andreas D., and Lavrov, Dennis V.
- Subjects
MNEMIOPSIS leidyi ,MITOCHONDRIAL DNA ,CTENOPHORA ,POLYMERASE chain reaction ,TRANSFER RNA ,LIGASES - Abstract
Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum-Ctenophora-has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we Polymerase Chain Reaction (PCR) amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10 kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, likely to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
85. RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria.
- Author
-
Rivera, Ajna S., Hammel, Jörg U., Haen, Karri M., Danka, Elizabeth S., Cieniewicz, Brandon, Winters, Ian P., Posfai, Dora, Wörheide, Gert, Lavrov, Dennis V., Knight, Scott W., Hill, Malcolm S., Hill, April L., and Nickel, Michael
- Subjects
RNA ,FUNGUS-bacterium relationships ,GENETIC regulation ,ACTIN ,PROTEIN genetics ,NUCLEIC acids - Abstract
Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from 'knocking down' expression of the actin gene. Conclusion: This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
86. The mitochondrial genomes of sponges provide evidence formultiple invasions by Repetitive Hairpin-forming Elements (RHE).
- Author
-
Erpenbeck, Dirk, Voigt, Oliver, Wörheide, Gert, and Lavrov, Dennis V.
- Subjects
GENOMES ,SPONGES (Invertebrates) ,MITOCHONDRIA ,DNA ,DEMOSPONGIAE - Abstract
Background: The mitochondrial (mt) genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida) and compare it with mtDNA of other sponges. Results: Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion: Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
87. Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae.
- Author
-
Xiujuan Wang and Lavrov, Dennis V.
- Subjects
- *
MITOCHONDRIAL DNA , *DEMOSPONGIAE , *GENOMES , *GENETICS , *BIOLOGICAL evolution , *TRANSFER RNA , *GENE rearrangement , *INTRONS , *NUCLEOTIDE sequence , *GENETIC code - Abstract
Two major transitions in animal evolution-the origins of multicellularity and bilaterality-correlate with major changes in mitochondrial DNA (mtDNA) organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13-15 protein genes, 2 rRNA genes, and 2-27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida). Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida) including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements, occurred in parallel in several lineages and suggest general trends in demosponge mtDNA evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
88. Mitochondrial Genome of the Homoscleromorph Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals.
- Author
-
Xiujuan Wang and Lavrov, Dennis V.
- Published
- 2007
89. The Complete Mitochondrial DNA Sequence of the Horseshoe Crab Limulus polyphemus.
- Author
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Lavrov, Dennis V., Boore, Jeffrey L., and Brown, Wesley M.
- Abstract
We determined the complete 14,985-nt sequence of the mitochondrial DNA of the horseshoe crab Limulus polyphemus (Arthropoda: Xiphosura). This mtDNA encodes the 13 protein, 2 rRNA, and 22 tRNA genes typical for metazoans. The arrangement of these genes and about half of the sequence was reported previously; however, the sequence contained a large number of errors, which are corrected here. The two strands of Limulus mtDNA have significantly different nucleotide compositions. The strand encoding most mitochondrial proteins has 1.25 times as many A's as T's and 2.33 times as many C's as G's. This nucleotide bias correlates with the biases in amino acid content and synonymous codon usage in proteins encoded by different strands and with the number of non–Watson-Crick base pairs in the stem regions of encoded tRNAs. The sizes of most mitochondrial protein genes in Limulus are either identical to or slightly smaller than those of their Drosophila counterparts. The usage of the initiation and termination codons in these genes seems to follow patterns that are conserved among most arthropod and some other metazoan mitochondrial genomes. The noncoding region of Limulus mtDNA contains a potential stem-loop structure, and we found a similar structure in the noncoding region of the published mtDNA of the prostriate tick Ixodes hexagonus. A simulation study was designed to evaluate the significance of these secondary structures; it revealed that they are statistically significant. No significant, comparable structure can be identified for the metastriate ticks Rhipicephalus sanguineus and Boophilus microplus. The latter two animals also share a mitochondrial gene rearrangement and an unusual structure of mt-tRNA(C) that is exactly the same association of changes as previously reported for a group of lizards. This suggests that the changes observed are not independent and that the stem-loop structure found in the noncoding regions of Limulus and Ixodes mtDNA may play the same role as that between trnN and trnC in vertebrates, i.e., the role of lagging strand origin of replication. [ABSTRACT FROM PUBLISHER]
- Published
- 2000
- Full Text
- View/download PDF
90. Pervasive mitochondrial tRNA gene loss in the clade B of haplosclerid sponges (Porifera, Demospongiae).
- Author
-
Lavrov DV, Turner TL, and Vicente J
- Abstract
Mitochondrial tRNA gene loss and cytosolic tRNA import are two common phenomena in mitochondrial biology, but their importance is often under-appreciated in animals. This is because the mitochondrial DNA (mtDNA) of most bilaterally symmetrical animals (Bilateria) encodes a complete set of tRNAs required for mitochondrial translation. By contrast, the mtDNA of non-bilaterian animals (phyla Cnidaria, Ctenophora, Porifera, and Placozoa) often contains a reduced set of tRNA genes, necessitating tRNA import from the cytosol. Interestingly, in many non-bilaterian lineages, tRNA gene content appears to be set early in evolution and remains conserved thereafter. Here, we report that Clade B of Haplosclerid Sponges (CBHS) represents an exception to this pattern, displaying considerable variation in tRNA gene content even among relatively closely related species. We determined mt-genome sequences for eight CBHS species and analyzed them in conjunction with six previously available sequences. Additionally, we sequenced mt-genomes for two species of haplosclerid sponges outside the CBHS and used eight previously available sequences as outgroups. We found that tRNA gene content varied widely within CBHS, ranging from three in an undescribed Haliclona species (Haliclona sp. TLT785) to 25 in Xestospongia muta and X. testudinaria. Furthermore, we found that all CBHS species outside the genus Xestospongia lacked the atp9 gene, with some also lacking atp8. Analysis of nuclear sequences from Niphates digitalis revealed that both atp8 and atp9 had transferred to the nuclear genome, while the absence of mt-tRNA genes indicated their genuine loss. We argue that CBHS can serve as a valuable system for studying mt-tRNA gene loss, mitochondrial import of cytosolic tRNAs, and the impact of these processes on mitochondrial evolution., (© The Author(s) 2025. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
- Published
- 2025
- Full Text
- View/download PDF
91. Expansion of the MutS gene family in plants.
- Author
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Sloan DB, Broz AK, Kuster SA, Muthye V, Peñafiel-Ayala A, Marron JR, Lavrov DV, and Brieba LG
- Abstract
The widely distributed MutS gene family functions in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded this gene family in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Cyanobacterial-like MutS1 and MutS2 genes were ancestrally gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae). Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing a name, "plant MSH1" is not directly related to the MSH1 gene in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotes. There has been substantial progress in understanding the functions of plant MSH1 and MSH6 genes, but the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are mitochondrial and/or plastid-targeted, the expansion of this family has played a large role in shaping plant organelle genetics., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)
- Published
- 2024
- Full Text
- View/download PDF
92. Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.
- Author
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Muthye V and Lavrov DV
- Subjects
- Animals, Computational Biology methods, Mitochondria metabolism, Proteomics methods, Software, Ctenophora metabolism, Ctenophora genetics, Proteome, Mitochondrial Proteins metabolism, Mitochondrial Proteins genetics
- Abstract
Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor., (© 2024. Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2024
- Full Text
- View/download PDF
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