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1. STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

   https://doi.org/10.1038/s41598-020-69101-z  

   Kitchen, S. A. ; Von Kuster, G. ; Kuntz, K. L. Vasquez ; Reich, H. G. ; Miller, W. ; Griffin, S. ; Fogarty, Nicole D. ; Baums, I. B. ( July 2020 , Scientific Reports)

   Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral,Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two CaribbeanAcroporaspecies as well as their dominant dinoflagellate symbiont,Symbiodinium ‘fitti’.SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the generaBreviolum, Cladocopium, andDurusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called theStandardTools forAcroporidGenotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporalmore »and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.

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2. Connecting the Light Curves of Type IIP Supernovae to the Properties of Their Progenitors

   https://doi.org/10.3847/1538-4357/ac77f3  

   Barker, Brandon L. ; Harris, Chelsea E. ; Warren, MacKenzie L. ; O’Connor, Evan P. ; Couch, Sean M. ( July 2022 , The Astrophysical Journal)

   Observations of core-collapse supernovae (CCSNe) reveal a wealth of information about the dynamics of the supernova ejecta and its composition but very little direct information about the progenitor. Constraining properties of the progenitor and the explosion requires coupling the observations with a theoretical model of the explosion. Here we begin with the CCSN simulations of Couch et al., which use a nonparametric treatment of the neutrino transport while also accounting for turbulence and convection. In this work we use the SuperNova Explosion Code to evolve the CCSN hydrodynamics to later times and compute bolometric light curves. Focusing on Type IIP SNe (SNe IIP), we then (1) directly compare the theoretical STIR explosions to observations and (2) assess how properties of the progenitor’s core can be estimated from optical photometry in the plateau phase alone. First, the distribution of plateau luminosities (L₅₀) and ejecta velocities achieved by our simulations is similar to the observed distributions. Second, we fit our models to the light curves and velocity evolution of some well-observed SNe. Third, we recover well-known correlations, as well as the difficulty of connecting any one SN property to zero-age main-sequence mass. Finally, we show that there is a usable, linearmore »correlation between iron core mass andL₅₀such that optical photometry alone of SNe IIP can give us insights into the cores of massive stars. Illustrating this by application to a few SNe, we find iron core masses of 1.3–1.5M_⊙with typical errors of 0.05M_⊙. Data are publicly available online on Zenodo: doi:10.5281/zenodo.6631964.

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3. Brothers Arc Flux

   https://doi.org/10.14379/iodp.proc.376.2019  

   de Ronde, C.E.J. ; Humphris, S.E. ; Höfig, T.W. ( July 2019 , Proceedings of the International Ocean Discovery Program)

   Volcanic arcs are the surface expression of magmatic systems that result from subduction of mostly oceanic lithosphere at convergent plate boundaries. Arcs with a submarine component include intraoceanic arcs and island arcs that span almost 22,000 km on Earth’s surface, and the vast majority of them are located in the Pacific region. Hydrothermal systems hosted by submarine arc volcanoes commonly contain a large component of magmatic fluid. This magmatic-hydrothermal signature, coupled with the shallow water depths of arc volcanoes and their high volatile contents, strongly influences the chemistry of the fluids and resulting mineralization and likely has important consequences for the biota associated with these systems. The high metal content and very acidic fluids in these hydrothermal systems are thought to be important analogs to numerous porphyry copper and epithermal gold deposits mined today on land. During International Ocean Discovery Program (IODP) Expedition 376 (5 May–5 July 2018), a series of five sites was drilled on Brothers volcano in the Kermadec arc. The expedition was designed to provide the missing link (i.e., the third dimension) in our understanding of hydrothermal activity and mineral deposit formation at submarine arc volcanoes and the relationship between the discharge of magmatic fluids and themore »deep biosphere. Brothers volcano hosts two active and distinct hydrothermal systems: one is seawater influenced and the other is affected by magmatic fluids (largely gases). In total, 222.4 m of volcaniclastics and lavas were recovered from the five sites drilled, which include Sites U1527 and U1530 in the Northwest (NW) Caldera seawater-influenced hydrothermal field; Sites U1528 and U1531 in the magmatic fluid-influenced hydrothermal fields of the Upper and Lower Cones, respectively; and Site U1529, located within an area of low crustal magnetization that marks the West (W) Caldera upflow zone on the caldera floor. Downhole logging and borehole fluid sampling were completed at two sites, and two tests of a prototype turbine-driven coring system (designed by the Center for Deep Earth Exploration [CDEX] at Japan Agency for Marine-Earth Science and Technology [JAMSTEC]) for drilling and coring hard rocks were conducted. Core recovered from all five sites consists of dacitic volcaniclastics and lava flows with only limited chemical variability relative to the overall range in composition of dacites in the Kermadec arc. Pervasive alteration with complex and variable mineral assemblages attest to a highly dynamic hydrothermal system. The upper parts of several drill holes at the NW Caldera hydrothermal field are characterized by secondary mineral assemblages of goethite + opal + zeolites that result from low-temperature (<150°C) reaction of rock with seawater. At depth, NW Caldera Site U1527 exhibits a higher temperature (~250°C) secondary mineral assemblage dominated by chlorite + quartz + illite + pyrite. An older mineral assemblage dominated by diaspore + quartz + pyrophyllite + rutile at the bottom of Hole U1530A is indicative of acidic fluids with temperatures of ~230°–320°C. In contrast, the alteration assemblage at Site U1528 on the Upper Cone is dominated by illite + natroalunite + pyrophyllite + quartz + opal + pyrite, which attests to high-temperature reaction of rocks with acid-sulfate fluids derived from degassed magmatic volatiles and the disproportionation of magmatic SO2. These intensely altered rocks exhibit extreme depletion of major cation oxides, such as MgO, K2O, CaO, MnO, and Na2O. Furthermore, very acidic (as low as pH 1.8), relatively hot (≤236°C) fluids collected at 160, 279, and 313 meters below seafloor in Hole U1528D have chemical compositions indicative of magmatic gas input. In addition, preliminary fluid inclusion data provide evidence for involvement of two distinct fluids: phase-separated (modified) seawater and a ~360°C hypersaline brine, which alters the volcanic rock and potentially transports metals in the system. The material and data recovered during Expedition 376 provide new stratigraphic, lithologic, and geochemical constraints on the development and evolution of Brothers volcano and its hydrothermal systems. Insights into the consequences of the different types of fluid–rock reactions for the microbiological ecosystem elucidated by drilling at Brothers volcano await shore-based studies.« less
4. Expedition 376 Preliminary Report: Brothers Arc Flux

   https://doi.org/10.14379/iodp.pr.376.2018  

   de Ronde, C.E.J. ; Humphris, S.E. ; Höfig, T.W. ( June 2019 , Preliminary report)

   Volcanic arcs are the surface expression of magmatic systems that result from the subduction of mostly oceanic lithosphere at convergent plate boundaries. Arcs with a submarine component include intraoceanic arcs and island arcs that span almost 22,000 km on Earth’s surface, the vast majority of which are located in the Pacific region. Hydrothermal systems hosted by submarine arc volcanoes commonly contain a large component of magmatic fluid. This magmatic-hydrothermal signature, coupled with the shallow water depths of arc volcanoes and their high volatile contents, strongly influences the chemistry of the fluids and resulting mineralization and likely has important consequences for the biota associated with these systems. The high metal contents and very acidic fluids in these hydrothermal systems are thought to be important analogs to numerous porphyry copper and epithermal gold deposits mined today on land. During International Ocean Discovery Program (IODP) Expedition 376 (5 May–5 July 2018), a series of five sites was drilled on Brothers volcano in the Kermadec arc. The expedition was designed to provide the missing link (i.e., the third dimension) in our understanding of hydrothermal activity and mineral deposit formation at submarine arc volcanoes and the relationship between the discharge of magmatic fluids and themore »deep biosphere. Brothers volcano hosts two active and distinct hydrothermal systems: one seawater-influenced and the other affected by magmatic fluids (largely gases). A total of 222.4 m of volcaniclastics and lavas was recovered from the five sites drilled, which include Sites U1527 and U1530 in the Northwest (NW) Caldera seawater-influenced hydrothermal field; Sites U1528 and U1531 in the magmatic fluid-influenced hydrothermal fields of the Upper and Lower Cones, respectively; and Site U1529, located in a magnetic low that marks the West (W) Caldera upflow zone on the caldera floor. Downhole logging and borehole fluid sampling were completed at two sites, and two tests of a prototype turbine-driven coring system (designed by the Center for Deep Earth Exploration [CDEX] at Japan Agency for Marine-Earth Science and Technology [JAMSTEC]) for drilling and coring hard rocks were conducted. Core recovered from all five sites consists of dacitic volcaniclastics and lava flows with only limited chemical variability relative to the overall range in composition of dacites in the Kermadec arc. Pervasive alteration with complex and variable mineral assemblages attest to a highly dynamic hydrothermal system. The upper parts of several drill holes at the NW Caldera hydrothermal field are characterized by secondary mineral assemblages of goethite + opal-A + zeolites that result from low-temperature (<150°C) reaction of rock with seawater. At depth, NW Caldera Site U1527 exhibits a higher temperature (~250°C) secondary mineral assemblage dominated by chlorite + quartz + illite + pyrite. An older mineral assemblage dominated by diaspore + quartz + pyrophyllite + rutile at the bottom of Hole U1530A is indicative of acidic fluids with temperatures of ~230°–320°C. By contrast, the alteration assemblage at Site U1528 on the Upper Cone is dominated by illite + natroalunite + pyrophyllite + quartz + opal-CT + pyrite, which attests to high-temperature reaction of rocks with acid-sulfate fluids derived from the disproportionation of magmatic SO2. These intensely altered rocks exhibit extreme depletion of major cation oxides, such as MgO, K2O, CaO, MnO, and Na2O. Furthermore, very acidic (as low as pH 1.8), relatively hot (≤247°C) fluids collected at depths of 160, 279, and 313 meters below seafloor (mbsf) in Hole U1528D have chemical compositions indicative of magmatic gas input. In addition, preliminary fluid inclusion data provide evidence for involvement of two distinct fluids: phase-separated (modified) seawater and an ~360°C hypersaline brine, altering the volcanic rock and potentially transporting metals in the system. The material and data recovered during Expedition 376 provide new stratigraphic, lithologic, and geochemical constraints on the development and evolution of Brothers volcano and its hydrothermal systems. Insights into the consequences of the different types of fluid-rock reactions for the microbiological ecosystem elucidated by drilling at Brothers await shore-based studies.« less
5. Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph

   https://doi.org/10.1186/s13015-021-00182-9  

   Mukherjee, Kingshuk ; Rossi, Massimiliano ; Salmela, Leena ; Boucher, Christina ( May 2021 , Algorithms for Molecular Biology)

   Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to asrmapper, and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) and Solve by Bionano Genomics on data from three genomes:E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was able to successfully run on all three genomes. The method ofmore »Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) only successfully ran onE. coli. Moreover, on the human genomermapperwas at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software,rmapperis written in C++ and is publicly available under GNU General Public License athttps://github.com/kingufl/Rmapper.

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