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Supporting data for "The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor"
<p>Methylome of the fresh water snail <em>Biomphalaria glabrata</em>. DNA was extracted from the feet of 10 individuals of <em>B. glabrata</em> originally isolated from Brazil. These snails have been cultivated in the laboratory since 1960. Tissue were grinded at 4°C and incubated in 1 ml volume of lysis buffer (20 mM TRIS pH 8; 1 mM EDTA; 100 mM NaCl; 0.5% SDS), with 0.3 mg of proteinase K at 55°C for 1 night. Afterwards, lysate was purified with phenol-chloroform and DNA was isopropanol precipitated. The extracted DNA (around 138ng/µL) was poled in equivalent amounts and Whole Genome Bisulfite Sequencing was done by GATC-biotech (www.gatc-biotech.com). The principle of this treatment is to convert non-methylated cytosines of gDNA into deoxy-uracil, whereas methylated cytosines remain intact. WGBS was done according to the Lister protocol (sequence 2 forward strands only). The reference genome (Biomphalaria-glabrata-BB02_SCAFFOLDS_BglaB1.fa) and annotation (Biomphalaria-glabrata-BB02_BASEFEATURES_BglaB1.3.gff3) used in this project are available on VectorBase (https://www.vectorbase.org/). To align our short reads, we chose to use two specific bisulfite mapping tools, BSMAP 1.0.0 (https://code.google.com/p/bsmap/) and Bismark 0.10.2 (www.bioinformatics.babraham.ac.uk /projects/bismark/), to compare their efficiency and convenience to finally work with the more suitable one on our datasets. IGV (Interactive Genomics Viewer, https://www.broadinstitute.org/igv/) was used to visualized final alignments.<br> BSMAP performed better than Bismark and was used for downstream analyses. Without default parameters alignement efficiency for BSMAP is 47.1%, allowing for 2 mismatches increases it to 55.6%. Methylation occurs predominantly in CpGs. (C methylated in CpG context: 12.4%, C methylated in CHG context: 0.5%, C methylated in CHH context: 0.5%) The major part of CpG sites, 95.7% were unmethylated, of the remaining 4.3% of CpG sites around 3.8% had low methylation, and 0.5% were completely methylated. Methylation is of the mosaic type. Methylation is relatively low with 1.2% of total cytosines. Our analyses suggested that conserved genes and genes with stable expression are localized in high methylated regions of the genome. Finally, we see that repetitive sequences were predominantly situated in low methylated regions of <em>B. glabrata</em>. </p> <p>Wiggle files were generated for CpG pairs only.</p> <p>Produced at IHPE (http://ihpe.univ-perp.fr/)</p>
Shell length and dry tissue weight relationship of the mollusk Ostrea lurida (Olympia Oyster) in the low and subtidal zones of the San Diego River, California: 2016-2017.
Data was collected to look at the relationship between the dry tissue weight and the shell length of Ostrea lurida in the San Diego River, and use the data to compare it to other estuaries O. lurida inhabit along the west coast of North America. Sampling was done in the low and sub intertidal zones along the delta of the San Diego River from October 2016 through September 2017. A fifty meter transect was chosen to collect samples which was broken up into five 10 meter transects. In each of these 10-m transects, 0.5 X 0.5 m quadrats were randomly selected for oyster assessments. Oysters were removed by physical removal by hand. Once back in the lab shell lengths were measured and dry weights were obtained.
Fiddler crab and mollusk density in experimentally manipulated tidal creeks off the Rowley River, (Rowley and Ipswich, MA)
Climate change is predicted to shift or extend the range of warm-water species poleward. In 2014, the fiddler crab was observed for the first time at the PIE LTER site in Northeast Massachusetts, which is north of its historical range. Beginning in 2014, density estimates were collected.
Mollusk from the Gulf of Mexico and Mexican Caribbean at the "Colección Regional de Moluscos de la Península de Yucatán" UMDI-Sisal, Facultad de Ciencias, UNAM, México.
<p>The dataset contains information about the “Colección Regional de Moluscos de la Península de Yucatán” (federal register INV-240-01-11) at the Unidad Multidisciplinaria de Docencia e Investigación, Faculty of Science, UNAM. This dataset represents only specimens of Phylum Mollusca identified to genus and species (3969 specimens) from 35 localities of the coast, coral reefs and deep-sea at the Gulf of Mexico and Mexican Caribbean for a period of time from 2007 to 2019. The dataset contains information on the specimens belonging to 166 families, 386 genus, and 542 species. The specimens at the collection have been either identified or validated by professional mollusk taxonomists, providing a significant level of trust in the data. The taxonomists that participated in this process appear in the list of authors.</p>
Fig. 14 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 14. Range chart of all taxa identified to genus or species level that have been described from Calcari a Lucina deposits. Not included are taxa reported by Moroni (1966) that we were not able to revise.
Fig. 13 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 13. The bivalve Sisonia ultimoi sp. nov. from the Middle Miocene Ca' Cavalmagra seep deposit in northern Italy. A. Left valve (MSF 1280). B. Small right valve (MSF 1265). C. Left valve (MSF 2372). D. Large right valve with severe shell injury (MSF 1278). E. Right valve (MSF 1281). F–G. Articulated specimen with broken posterior end (MSF 2367). H–I. Holotype (MGGC 22330), articulated specimen showing outline of shell. J–K. Paratype, articulated specimen with deformed posterior side, showing the regular commarginal ornament; this specimen preserves the most realistic inflation of all available specimens (MSF 2368). L–M. Articulated specimen (MSF 2369). N–O. Articulated specimen showing fine internal striation (MSF 2370). P–Q. Deformed specimen showing the regular commarginal ornament (MSF 2371).
Fig. 11 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 11. The lucinid bivalve Miltha? romaniae sp. nov., from the Ca' Cassano seep deposit in northern Italy. A. Paratype (MSF 2345). B. Paratype (MSF 2347). C. Holotype (MSF 2346). D–F. Paratype with well-preserved ventral side (MSF 2362). D. Ventral view showing the slight undulation of the ventral margin. E. Posteroventral surface showing the increasing strength and spacing of the commarginal ribs. F. Close-up on anteroventral surface, showing the fine obliquely tangential thread-like ridges. G. Paratype (MSF 2363), right valve embedded in rock matrix, showing the aams.
Fig. 9. Thyasirid bivalves from Calcari a in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 9. Thyasirid bivalves from Calcari a Lucina seep deposits in northern Italy. A–B. Thyasira sp. 1, Castiglione dei Pepoli (MGGC 22311). C. Thyasira sp. 2, Casola (MGGC 22312). D–E. Channelaxinus? sp., Caselle A (NRM Mo 204840).
Fig. 8. Protobranch bivalves from Calcari a in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 8. Protobranch bivalves from Calcari a Lucina seep deposits in northern Italy. A–D. The nuculid Nucula aff. sulcata Bronn, 1831. A. MSF 2366. B. Right valve from Le Colline (MSF 1212). C. Right valve from Le Colline (MSF 1210). D. Left valve from Ca' Cavalmagra (MSF 1311). E–F. The solemyid Acharax doderleini (Mayer, 1861) from Ca' Fornace erratics. E. External mold of right valve (MSF 2361). F. Internal mold of right valve (MSF 2360).
Fig. 12. Vesicomyid bivalves from Miocene Calcari a in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 12. Vesicomyid bivalves from Miocene Calcari a Lucina seep deposits in northern Italy. A–H. Archivesica strigarum Kiel & Taviani, 2017. A–B. Articulated specimen from Caselle A (NRM Mo 204841). C. Hinge of RV (Caselle A, NRM Mo 204842). D. Hinge of LV (Caselle A, NRM Mo 204843). E. Articulated specimen from Casola showing ligament (MGGC 22325). F. Articulated specimen from Casola, view on RV showing anterior adductor muscle scar (MGGC 22326). G. Internal mold of RV showing muscle scars and pallial line, from Castillon dei Pepoli (MGGC 22323).H. Left valve with shell remains, from Casola (MGGC 22324). I–J. Wareniconcha? sp., external view on articulated specimen from Castel di Casio (MGGC 22329).
Fig. 4. Calliostomatidae Thiele, 1924 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 4. Calliostomatidae Thiele, 1924 (1847) (Vetigastropoda) from the Calcari a Lucina seep deposits in northern Italy. A–C. Calliostoma sp., Le Colline (MSF 1207). D–F. Calliostoma? sp., Le Colline (MSF 1208).
Fig. 6 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 6. Neritimorpha Golikov & Starobogatov, 1975 and Caenogastropoda Cox, 1960 from the Calcari a Lucina seep deposits in northern Italy. A–B. The phenacolepid (Neritimorpha) Thalassonerita megastoma Moroni, 1966, Le Colline (MSF 1223), internal mold showing columellar muscle scars. C–E. The elachisinid (Caenogastropoda) Laeviphitus sp. C. Small specimen with preserved protoconch, from Ca' Rovereti (NRM Mo 204837). D. Close-up on transition between proto- and teleoconch, from Ca' Rovereti (NRM Mo 204838). E. Tall specimen (MSF 1204) from Le Colline. F–G. Naticidae indet. sp. 1. F. Shell embedded in rock matrix, from Castiglion dei Pepoli (MGGC 22304). G. Operculum (MSF 1218). H. Naticidae indet. sp. 2 from Guzzano (MGGC 22305). I–K. Pisanianura? pusilla Bellardi 1872, from Castel di Casio. I. Specimen with remains of siphonal canal and shell sculpture (MGGC 22306). J. Small, internal mold (MGGC 22307). K. Large specimen with preserved shell (MGGC 22308). L. Semicassis aff. reticulata (Bellardi & Michelotti, 1840), Castiglion dei Pepoli (MGGC 22310).
Fig. 7. Neogastropoda Wenz, 1938 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 7. Neogastropoda Wenz, 1938 and Heterobranchia Burmeister, 1837 from Miocene Calcari a Lucina seep deposits in northern Italy. A–C. The eosiphonid Eosipho hoernesi (Bellardi, 1872). A–B. Specimen with well-preserved aperture, from Ca' Piantè (MSF 1070). C. Specimen showing details of spiral ornament, from Ca' Rovereti (NRM Mo 204839). D. The buccinid Neptunea? sp. from Le Colline (MSF 2359). E–F. The olivid Olivella longispira Bellardi, 1882. E. From Le Colline (MSF 1202). F. From Guzzano (MGGC 22310). G. The turrid Turris citima (Bellardi, 1877), from Ca' Cavalmagra (MSF 1307). H–I. The turrid Turricula sp., from Ca' Piantè (MSF 1081). J. The pyramidellid (Heterobranchia) Turbonilla sp., from Ca' Cavalmagra (MSF 1305).
Fig. 5 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 5. Vetigastropoda Salvini-Plawen, 1980, Patellogastropoda Lindberg, 1986 and Neomphalina McLean, 1981 from the Calcari a Lucina seep deposits in northern Italy. A–G. The colloniid (Vetigastropoda) Homalopoma domeniconii Moroni, 1966. A–B. MSF 2357 from Ca' Piantè. C–D. MSF 2365 from Ca' Piantè. E–G. MSF 1216 from Le Colline. H–L. The fissurellid (Vetigastropoda) Fissurella costicillatissima Sacco, 1897, from Le Colline. H–I. Specimen with remnants of surface sculpture (MSF 1214). J–L. Internal mold showing mantle attachment scars and foramen (MSF 1213). M–N. The lottiid (Patellogastropoda) Tectura? cf. taurinensis Sacco, 1897, from Ca' Cavalmagra (MSF 1310). O–Q. The neomphaline Retiskenea? sp. from Ca' Cavalmagra. O–P. MSF 2364. Q. MSF 1312.
Fig. 3. Chilodontaidae Wenz, 1938 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 3. Chilodontaidae Wenz, 1938 (Vetigastropoda) from the Miocene Calcari a Lucina seep deposits in northern Italy. A–C. Putzeysia diversii sp. nov. A–B. Holotype, Ca' Piantè (MSF 1079). C. Paratype, Ca' Cavalmagra (MSF 1300). D–F. Chilodontaidae indet., Le Colline (MSF 1209).
Fig. 1 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 1. Sampling sites in northern Italy. A. Their locations in northern Italy, numbers correspond to those in panel B. B. Stratigraphic ages of the sampling sites. Map produced using the GeoMapApp (https://www.geomapapp.org/, Ryan et al. 2009).
Fig. 2. Seguenzioidea A.E. Verrill, 1884 in Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions
Fig. 2. Seguenzioidea A.E. Verrill, 1884 (Vetigastropoda) from the Calcari a Lucina seep deposits in northern Italy. A–J. The cataegid Cataegis taurocrassa (Sacco, 1895). A–D. Complete specimen from Le Colline (MSF 1230). E–F. Specimen partly embedded in rock matrix (MSF 2351). G–H. Complete specimen from Ca' Piantè (MSF 2352). I–J. Complete specimen from Ca' Piantè (MSF 2353). K–L. The calliotropid Calliotropis sp. from Ca' Piantè (MSF 1076).
РИС. 1. Схематичное иЗображение глаЗа наЗемного лёгочного моллюска. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела; L abs – абсолютное расстоЯние между Зрачком и наружной поверхностью хрусталика; D l – продольный диаметр хрусталика; А – абсолютный диаметр Зрачabs ка; D – поперечный диаметр глаЗа. FIG. 1. Schematic drawing of the eye of a terrestrial pulmonate mollusk. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body; L abs – the absolute distance between the pupil and the outer surface of the lens; D l – the longitudinal diameter of the lens; А abs – the absolute diameter of the pupil; D e – the transverse diameter of the eye. in Зрачок камерных глаЗ наЗемных брюхоногих моллюсков (Heterobranchia, Stylommatophora)
РИС. 1. Схематичное иЗображение глаЗа наЗемного лёгочного моллюска. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела; L abs – абсолютное расстоЯние между Зрачком и наружной поверхностью хрусталика; D l – продольный диаметр хрусталика; А – абсолютный диаметр Зрачabs ка; D – поперечный диаметр глаЗа. FIG. 1. Schematic drawing of the eye of a terrestrial pulmonate mollusk. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body; L abs – the absolute distance between the pupil and the outer surface of the lens; D l – the longitudinal diameter of the lens; А abs – the absolute diameter of the pupil; D e – the transverse diameter of the eye.
РИС. 1. ОЗеро Дальнее (А) и место обнаруЖениЯ Beringiana beringiana в оЗере (B, С), песчаный грунт в месте обитаниЯ беЗЗубок (D). Стрелками обоЗначено место сбора моллюсков. FIG. 1. Lake Dalneye (A) with the sampling site (B, C), sandy bottom in the habitat of mollusks (D). The arrows indicate the site of material sampling. in Первые данные о морфологии глохидиев двустворчатых моллюсков Beringiana beringiana (Bivalvia, Unionidae) оЗера Дальнее, Камчатка
РИС. 1. ОЗеро Дальнее (А) и место обнаруЖениЯ Beringiana beringiana в оЗере (B, С), песчаный грунт в месте обитаниЯ беЗЗубок (D). Стрелками обоЗначено место сбора моллюсков. FIG. 1. Lake Dalneye (A) with the sampling site (B, C), sandy bottom in the habitat of mollusks (D). The arrows indicate the site of material sampling.
Рис. 8. СреЗы череЗ гонады моллюска: А – поперечный среЗ череЗ гонаду самки, Б–Д – фолликулы в гонадах самок (Б, В – Зрелые ооциты круглой формы, готовые к вымету; Г – ооциты в период активного гаметогенеЗа на стадии раннего трофоплаЗматического роста, Д – ооциты каплевидной формы в период преднерестовой стадии при ЗаверШении трофоплаЗматического роста), Е, Ж – поперечные среЗы череЗ гонаду самца, З, И – ацинусы в гонадах самцов (З – преднерестоваЯ стадиЯ, просветы в ацинусах практически отсутствуют, стенки ацинусов не раЗличимы, И – нерестоваЯ стадиЯ, имеютсЯ просветы в ацинусах). МасШтабные линейки 300 мкм (А), 200 мкм (Е), 100 мкм (Ж), 50 мкм (Б–Д, З, И). вя – вакуолиЗированное Ядро, сф – стенка фолликула, вм – вителлиноваЯ мембрана, РО – раЗвиваюЩиесЯ иЗ пелликулы ооциты, пг – ресничный проток гонады, с – сперматоциты, па – просветы в ацинусах. Fig. 8. Sections through the gonads of the mollusk: А – transverse section through the female gonad, Б–Д – ovarian acini, follicles (Б, В – mature round-shaped oocytes ready to be swept out; Г – oocytes in the period of active gametogenesis at the stage of early trophoplasmatic growth, Д – tear-shaped oocytes during the pre-spawning stage at the end of trophoplasmatic growth), Е, Ж – transverse sections through the male gonads, З, И – testicular acini (З – pre-spawning stage, with practically absent gaps in the acini and invisible the acini walls, И – spawning stage, with gaps in the acini). Scale bars 300 µm (A), 200 µm (E), 100 µm (Ж), 50 µm (Б–Д, З, И). вя – vacuolated nucleus, сф – follicle wall, вм – vitelline membrane, РО – developing oocytes arising from a pellicle, пг – ciliated gonadal duct, с – spermatocytes, па – gaps in acini. in Nodularia vladivostokensis (Bivalvia: Unionidae) from Razdolnaya River (Primorye, Russia)
Рис. 8. СреЗы череЗ гонады моллюска: А – поперечный среЗ череЗ гонаду самки, Б–Д – фолликулы в гонадах самок (Б, В – Зрелые ооциты круглой формы, готовые к вымету; Г – ооциты в период активного гаметогенеЗа на стадии раннего трофоплаЗматического роста, Д – ооциты каплевидной формы в период преднерестовой стадии при ЗаверШении трофоплаЗматического роста), Е, Ж – поперечные среЗы череЗ гонаду самца, З, И – ацинусы в гонадах самцов (З – преднерестоваЯ стадиЯ, просветы в ацинусах практически отсутствуют, стенки ацинусов не раЗличимы, И – нерестоваЯ стадиЯ, имеютсЯ просветы в ацинусах). МасШтабные линейки 300 мкм (А), 200 мкм (Е), 100 мкм (Ж), 50 мкм (Б–Д, З, И). вя – вакуолиЗированное Ядро, сф – стенка фолликула, вм – вителлиноваЯ мембрана, РО – раЗвиваюЩиесЯ иЗ пелликулы ооциты, пг – ресничный проток гонады, с – сперматоциты, па – просветы в ацинусах. Fig. 8. Sections through the gonads of the mollusk: А – transverse section through the female gonad, Б–Д – ovarian acini, follicles (Б, В – mature round-shaped oocytes ready to be swept out; Г – oocytes in the period of active gametogenesis at the stage of early trophoplasmatic growth, Д – tear-shaped oocytes during the pre-spawning stage at the end of trophoplasmatic growth), Е, Ж – transverse sections through the male gonads, З, И – testicular acini (З – pre-spawning stage, with practically absent gaps in the acini and invisible the acini walls, И – spawning stage, with gaps in the acini). Scale bars 300 µm (A), 200 µm (E), 100 µm (Ж), 50 µm (Б–Д, З, И). вя – vacuolated nucleus, сф – follicle wall, вм – vitelline membrane, РО – developing oocytes arising from a pellicle, пг – ciliated gonadal duct, с – spermatocytes, па – gaps in acini.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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