المؤلفون: Nicolas Locatelli, Kitchen, Sheila, Stankiewicz, Kathryn, Baums, Iliana

الوصف: Initial Release of Acropora palmata and Acropora cervicornis genome assemblies, genetic maps, gene predictions, and functional annotations. Here, we make available the code and genomic resources described in Locatelli et al., 2023. These files describe the genomic resources for Florida Acropora palmata sampled at Horseshoe Reef (genet HS1, STAGdb ID HG0004) and Acropora cervicornis sampled from Grassy Key (genet M5, STAGdb ID HG0005). All tissue samples were generously provided by the Coral Restoration Foundation™ (CRF). In jupyter_notebooks/, we provide code for Acropora cervicornis (prefix Acervicornis in all files) genome assembly, gene prediction, and functional annotation in FunAnnotate. We additionally provide code for Acropora palmata (prefix Apalmata in all files) and Acropora cervicornis linkage map generation using LepWrap. Further, we provide code for some figure generation, whole genome alignments and dotplots, and phylogenetically significant gene family expansion analyses (CAFE5). In ...

العلاقة: https://github.com/mistergroot/apal_acer_genomes/tree/v1.0.0Test; https://dx.doi.org/10.5281/zenodo.12021087Test

الإتاحة: https://doi.org/10.5281/zenodo.1202108610.5281/zenodo.12021087Test

المؤلفون: Kitchen, Sheila A., Naragon, Thomas H., Brückner, Adrian, Ladinsky, Mark S., Quinodoz, Sofia A., Badroos, Jean M., Viliunas, Joani W., Kishi, Yuriko, Wagner, Julian M., Miller, David R., Yousefelahiyeh, Mina, Antoshechkin, Igor A., Eldredge, K. Taro, Pirro, Stacy, Guttman, Mitchell, Davis, Steven R., Aardema, Matthew L., Parker, Joseph

المصدر: Cell, 187(14), 1-22, (2024-07-11)

الوصف: How evolution at the cellular level potentiates macroevolutionary change is central to understanding biological diversification. The >66,000 rove beetle species (Staphylinidae) form the largest metazoan family. Combining genomic and cell type transcriptomic insights spanning the largest clade, Aleocharinae, we retrace evolution of two cell types comprising a defensive gland—a putative catalyst behind staphylinid megadiversity. We identify molecular evolutionary steps leading to benzoquinone production by one cell type via a mechanism convergent with plant toxin release systems, and synthesis by the second cell type of a solvent that weaponizes the total secretion. This cooperative system has been conserved since the Early Cretaceous as Aleocharinae radiated into tens of thousands of lineages. Reprogramming each cell type yielded biochemical novelties enabling ecological specialization—most dramatically in symbionts that infiltrate social insect colonies via host-manipulating secretions. Our findings uncover cell type evolutionary processes underlying the origin and evolvability of a beetle chemical innovation. ; © 2024 Elsevier. ; We thank Charlie Barnes, Mike Caterino, Munetoshi Maruyama, Thomas Schmitt, and Christoph von Beeren for beetle specimens; Taku Shimada and Udo Schmidt forDalotia photography and specimen images; Nathan Dalleska (Water and Environment lab, Caltech) for HPLC assistance, and Elizabeth Soehalim for help with SPRITE. We acknowledge support from Caltech's Center for Evolutionary Science. A.B. was a Simons Fellow of the Life Sciences Research Foundation. J.M.W. and J.W.V. are NSF GRFP recipients. This work was funded by grants to J.P. from the NIH (1R34NS118470-01), NSF (2047472 CAREER), along with a Shurl and Kay Curci Foundation grant, Rita Allen Foundation Scholarship, Pew Biomedical Scholarship, and an Alfred P. Sloan Foundation fellowship. Additional funding was provided by Iridian Genomes (IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa), Caltech’s Millard and Muriel Jacobs ...

العلاقة: https://www.caltech.edu/about/news/beetles-conquered-earth-by-evolving-their-own-biochemical-laboratoryTest; https://doi.org/10.1016/j.cell.2024.05.012Test; oai:authors.library.caltech.edu:8n92k-h7b39

الإتاحة: https://doi.org/10.1016/j.cell.2024.05.012Test

المؤلفون: Blanco-Pimentel, Macarena, Kenkel, Carly D., Kitchen, Sheila A., Calle-Triviño, Johanna, Baums, Iliana B., Cortés-Useche, Camilo, Morikawa, Megan K.

المصدر: Blanco-Pimentel , M , Kenkel , C D , Kitchen , S A , Calle-Triviño , J , Baums , I B , Cortés-Useche , C & Morikawa , M K 2024 , ' Overcoming barriers to reef restoration : Field-based method for approximate genotyping of Acropora cervicornis ' , Restoration Ecology , vol. 32 , no. 3 , e14073 . https://doi.org/10.1111/rec.14073Test

مصطلحات موضوعية: 2b-RAD, Caribbean, coral histocompatibility, genetic distance, genotypic diversity, grafting method, SNP-chip

الوصف: Reef restoration efforts aim to enhance resilience by safeguarding the genetic diversity of coral populations. This could be facilitated by genotyping methods that are relatively inexpensive, and field-based. A potential method for assessing coral genotypic diversity arises from self-recognition phenomena. Past studies have shown that contact between tissues from the same genet (isogeneic) will fuse whereas tissue from different genets (allogeneic) will result in rejection. However, the accuracy of this method has been questioned. Here, we revisit the grafting method as a tool to estimate genotypic diversity in a Caribbean coral restoration target, Acropora cervicornis. Ten ramets of unknown genetic relation were arranged in 82 grafting tests consisting of 5-fragment bundles that replicated all possible combinations between ramets. After 10 weeks, we found that outcomes of acceptance and rejection were highly consistent (96.7% across all combinations and replicates). The proposed existence of 4 genets across the 10 ramets based on response outcomes was confirmed by two SNP-based genotyping methods. Both genet pairing (isogeneic or allogeneic pairs) and genetic distance significantly affected the odds of acceptance or rejection responses. Moreover, a significant correlation was found between the degree of fusion between fragments and their genetic distance, supporting that the most related ramets are accepted more strongly compared to those that are more unrelated. This field-based contact method can be a powerful tool to estimate genotypic diversity in coral nurseries, facilitating the management of genetic diversity within the nursery and genotype-level tracking of key traits like disease and bleaching resistance.

وصف الملف: application/pdf

العلاقة: https://research.rug.nl/en/publications/ce7b2063-7866-429f-836b-b6b0643748efTest

الإتاحة: https://doi.org/10.1111/rec.14073Test
https://hdl.handle.net/11370/ce7b2063-7866-429f-836b-b6b0643748efTest
https://research.rug.nl/en/publications/ce7b2063-7866-429f-836b-b6b0643748efTest
https://pure.rug.nl/ws/files/937604136/Restoration_Ecology_-_2023_-_Blanco_Pimentel_-_Overcoming_barriers_to_reef_restoration_field_based_method_for_approximate.pdfTest
http://www.scopus.com/inward/record.url?scp=85179335071&partnerID=8YFLogxKTest

المؤلفون: Davies, Sarah W., Gamache, Matthew H., Howe-Kerr, Lauren I., Kriefall, Nicola G., Baker, Andrew C., Banaszak, Anastazia T., Bay, Line Kolind, Bellantuono, Anthony J., Bhattacharya, Debashish, Chan, Cheong Xin, Claar, Danielle C., Coffroth, Mary Alice, Cunning, Ross, Davy, Simon K., Campo, Javier del, Díaz-Almeyda, Erika M., Frommlet, Jörg C., Fuess, Lauren E., González-Pech, Raúl A., Goulet, Tamar L., Hoadley, Kenneth D., Howells, Emily J., Hume, Benjamin C. C., Kemp, Dustin W., Kenkel, Carly D., Kitchen, Sheila A., LaJeunesse, Todd C., Lin, Senjie, McIlroy, Shelby E., McMinds, Ryan, Nitschke, Matthew R., Oakley, Clinton A., Peixoto, Raquel S., Prada, Carlos, Putnam, Hollie M., Quigley, Kate, Reich, Hannah G., Reimer, James Davis, Rodriguez-Lanetty, Mauricio, Rosales, Stephanie M., Saad, Osama S., Sampayo, Eugenia M., Santos, Scott R., Shoguchi, Eiichi, Smith, Edward G., Stat, Michael, Stephens, Timothy G., Strader, Marie E., Suggett, David J., Swain, Timothy D., Tran, Cawa, Traylor-Knowles, Nikki, Voolstra, Christian R., Warner, Mark E., Weis, Virginia M., Wright, Rachel M., Xiang, Tingting, Yamashita, Hiroshi, Ziegler, Maren, Correa, Adrienne M. S., Parkinson, John Everett

الوصف: Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

وصف الملف: application/pdf

العلاقة: Davies, Sarah W., Gamache, Matthew H., Howe-Kerr, Lauren I., et al. "Building consensus around the assessment and interpretation of Symbiodiniaceae diversity." PeerJ, 11, (2023) PeerJ, Inc: https://doi.org/10.7717/peerj.15023Test.; https://hdl.handle.net/1911/115006Test; peerj-15023; https://doi.org/10.7717/peerj.15023Test

الإتاحة: https://doi.org/10.7717/peerj.15023Test
https://hdl.handle.net/1911/115006Test

المؤلفون: Stankiewicz, Kathryn H., Guiglielmoni, Nadège, Kitchen, Sheila A., Flot, Jean-François, Barott, Katie L., Davies, Sarah W., Finnerty, John R., Grace, Sean P., Kaufman, Leslie S., Putnam, Hollie M., Rotjan, Randi D., Sharp, Koty H., Baums, Iliana B.

الوصف: Facultatively symbiotic corals provide important experimental models to explore the establishment, maintenance, and breakdown of the mutualism between corals and members of the algal family Symbiodiniaceae. The temperate coral Astrangia poculata is one such model as it is not only facultatively symbiotic, but also occurs across a broad temperature and latitudinal gradient. Here, we report the de novo chromosome-scale assembly and annotation of the A. poculata genome. Though widespread segmental/tandem duplications of genomic regions were detected, we did not find strong evidence of a whole genome duplication (WGD) event. Comparison of the gene arrangement between A. poculata and the tropical coral Acropora millepora revealed 56.38% of the orthologous genes were conserved in syntenic blocks despite ~415 million years of divergence. Gene families related to sperm hyperactivation and innate immunity, including lectins, were found to contain more genes in A. millepora relative to A. poculata. Sperm hyperactivation in A. millepora is expected given the extreme requirements of gamete competition during mass spawning events in tropical corals, while lectins are important in the establishment of coral-algal symbiosis. By contrast, gene families involved in sleep promotion, feeding suppression, and circadian sleep/wake cycle processes were expanded in A. poculata. These expanded gene families may play a role in A. poculata’s ability to enter a dormancy-like state (“winter quiescence”) to survive freezing temperatures at the northern edges of the species’ range. ; IOS-1354935 - National Science Foundation ; First author draft

العلاقة: bioRxiv; K.H. Stankiewicz, N. Guiglielmoni, S.A. Kitchen, J.-F. Flot, K.L. Barott, S.W. Davies, J.R. Finnerty, S.P. Grace, L.S. Kaufman, H.M. Putnam, R.D. Rotjan, K.H. Sharp, I.B. Baums. "Genomic comparison of the temperate coral Astrangia poculata with tropical corals yields insights into winter quiescence, innate immunity, and sexual reproduction" bioRxiv. https://doi.org/10.1101/2023.09.22.558704Test; https://hdl.handle.net/2144/48539Test; 0000-0001-8576-6774 (Finnerty, John R); 893809

الإتاحة: https://doi.org/10.1101/2023.09.22.558704Test
https://hdl.handle.net/2144/48539Test

المؤلفون: Blanco‐Pimentel, Macarena, Kenkel, Carly D., Kitchen, Sheila A., Calle‐Triviño, Johanna, Baums, Iliana B., Cortés‐Useche, Camilo, Morikawa, Megan K.

المصدر: Restoration Ecology ; volume 32, issue 3 ; ISSN 1061-2971 1526-100X

الوصف: Reef restoration efforts aim to enhance resilience by safeguarding the genetic diversity of coral populations. This could be facilitated by genotyping methods that are relatively inexpensive, and field‐based. A potential method for assessing coral genotypic diversity arises from self‐recognition phenomena. Past studies have shown that contact between tissues from the same genet (isogeneic) will fuse whereas tissue from different genets (allogeneic) will result in rejection. However, the accuracy of this method has been questioned. Here, we revisit the grafting method as a tool to estimate genotypic diversity in a Caribbean coral restoration target, Acropora cervicornis . Ten ramets of unknown genetic relation were arranged in 82 grafting tests consisting of 5‐fragment bundles that replicated all possible combinations between ramets. After 10 weeks, we found that outcomes of acceptance and rejection were highly consistent (96.7% across all combinations and replicates). The proposed existence of 4 genets across the 10 ramets based on response outcomes was confirmed by two SNP‐based genotyping methods. Both genet pairing (isogeneic or allogeneic pairs) and genetic distance significantly affected the odds of acceptance or rejection responses. Moreover, a significant correlation was found between the degree of fusion between fragments and their genetic distance, supporting that the most related ramets are accepted more strongly compared to those that are more unrelated. This field‐based contact method can be a powerful tool to estimate genotypic diversity in coral nurseries, facilitating the management of genetic diversity within the nursery and genotype‐level tracking of key traits like disease and bleaching resistance.

الإتاحة: https://doi.org/10.1111/rec.14073Test

المؤلفون: Ashley, Immy A., Kitchen, Sheila A., Gorman, Lucy M., Grossman, Arthur R., Oakley, Clinton A., Suggett, David J., Weis, Virginia M., Rosset, Sabrina L., Davy, Simon K.

المساهمون: Marsden Fund, Victoria University of Wellington, Australian Research Council, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

المصدر: Frontiers in Microbiology ; volume 13 ; ISSN 1664-302X

مصطلحات موضوعية: Microbiology (medical), Microbiology

الوصف: The mutualistic cnidarian–dinoflagellate symbiosis underpins the evolutionary success of stony corals and the persistence of coral reefs. However, a molecular understanding of the signalling events that lead to the successful establishment and maintenance of this symbiosis remains unresolved. For example, the phosphatidylinositol (PI) signalling pathway has been implicated during the establishment of multiple mutualistic and parasitic interactions across the kingdoms of life, yet its role within the cnidarian-dinoflagellate symbiosis remains unexplored. Here, we aimed to confirm the presence and assess the specific enzymatic composition of the PI signalling pathway across cnidaria and dinoflagellates by compiling 21 symbiotic anthozoan (corals and sea anemones) and 28 symbiotic dinoflagellate (Symbiodiniaceae) transcriptomic and genomic datasets and querying genes related to this pathway. Presence or absence of PI-kinase and PI-phosphatase orthologs were also compared between a broad sampling of taxonomically related symbiotic and non-symbiotic species. Across the symbiotic anthozoans analysed, there was a complete and highly conserved PI pathway, analogous to the pathway found in model eukaryotes. The Symbiodiniaceae pathway showed similarities to its sister taxon, the Apicomplexa, with the absence of PI 4-phosphatases. However, conversely to Apicomplexa, there was also an expansion of homologs present in the PI5-phosphatase and PI5-kinase groups, with unique Symbiodiniaceae proteins identified that are unknown from non-symbiotic unicellular organisms. Additionally, we aimed to unravel the putative functionalities of the PI signalling pathway in this symbiosis by analysing phosphoinositide (PIP)-binding proteins. Analysis of phosphoinositide (PIP)-binding proteins showed that, on average, 2.23 and 1.29% of the total assemblies of anthozoan and Symbiodiniaceae, respectively, have the potential to bind to PIPs. Enrichment of Gene Ontology (GO) terms associated with predicted PIP-binding proteins within each taxon ...

الإتاحة: https://doi.org/10.3389/fmicb.2022.1094255Test

المؤلفون: Baums, Iliana B., Baker, Andrew C., Davies, Sarah W., Grottoli, Andréa G., Kenkel, Carly D., Kitchen, Sheila A., Kuffner, Ilsa B., LaJeunesse, Todd C., Matz, Mikhail V., Miller, Margaret W., Parkinson, John E., Shantz, Andrew A.

المصدر: Ecological Applications, 2019 Dec 01. 29(8), 1-23.

الوصول الحر: https://www.jstor.org/stable/26851849Test

المؤلفون: Blanco‐Pimentel, Macarena, Kenkel, Carly D., Kitchen, Sheila A., Calle‐Triviño, Johanna, Baums, Iliana B., Cortés‐Useche, Camilo, Morikawa, Megan K.

المصدر: Restoration Ecology; Mar2024, Vol. 32 Issue 3, p1-12, 12p

مصطلحات موضوعية: ACROPORA, GENETIC distance, GENETIC variation, REEFS, NATURAL immunity

مستخلص: Reef restoration efforts aim to enhance resilience by safeguarding the genetic diversity of coral populations. This could be facilitated by genotyping methods that are relatively inexpensive, and field‐based. A potential method for assessing coral genotypic diversity arises from self‐recognition phenomena. Past studies have shown that contact between tissues from the same genet (isogeneic) will fuse whereas tissue from different genets (allogeneic) will result in rejection. However, the accuracy of this method has been questioned. Here, we revisit the grafting method as a tool to estimate genotypic diversity in a Caribbean coral restoration target, Acropora cervicornis. Ten ramets of unknown genetic relation were arranged in 82 grafting tests consisting of 5‐fragment bundles that replicated all possible combinations between ramets. After 10 weeks, we found that outcomes of acceptance and rejection were highly consistent (96.7% across all combinations and replicates). The proposed existence of 4 genets across the 10 ramets based on response outcomes was confirmed by two SNP‐based genotyping methods. Both genet pairing (isogeneic or allogeneic pairs) and genetic distance significantly affected the odds of acceptance or rejection responses. Moreover, a significant correlation was found between the degree of fusion between fragments and their genetic distance, supporting that the most related ramets are accepted more strongly compared to those that are more unrelated. This field‐based contact method can be a powerful tool to estimate genotypic diversity in coral nurseries, facilitating the management of genetic diversity within the nursery and genotype‐level tracking of key traits like disease and bleaching resistance. [ABSTRACT FROM AUTHOR]

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المؤلفون: Brückner, Adrian, Barnett, Austen A., Bhat, Prashant, Antoshechkin, Igor A., Kitchen, Sheila A.

المصدر: Acarologia 62(2) 532-573

مصطلحات موضوعية: Biodiversity, Taxonomy, Animalia, Arthropoda, Arachnida, Sarcoptiformes, Trhypochthoniidae

الوصف: Brückner, Adrian, Barnett, Austen A., Bhat, Prashant, Antoshechkin, Igor A., Kitchen, Sheila A. (2022): Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus. Acarologia 62 (2): 532-573, DOI:10.24349/pjye-gkeo, URL: https://www1.montpellier.inrae.fr/CBGP/acarologia/article.php?id=4528Test

العلاقة: info:eu-repo/semantics/altIdentifier/lsid/urn:lsid:plazi.org:pub:FFD1FFBA5235FFD1FFC6FFAFF96ACE25; info:eu-repo/semantics/altIdentifier/url/http://publication.plazi.org/id/FFD1FFBA5235FFD1FFC6FFAFF96ACE25Test; http://treatment.plazi.org/id/03E887C25230FFD7FE2DFC37FBB6CC37Test; http://treatment.plazi.org/id/03E887C2523EFFDDFE2DFBC4FD27CA46Test; https://zenodo.org/communities/biosyslitTest; https://zenodo.org/record/7160532Test; https://doi.org/10.24349/pjye-gkeoTest; oai:zenodo.org:7160532

الإتاحة: https://doi.org/10.24349/pjye-gkeoTest
https://doi.org/10.5281/zenodo.7160534Test
https://doi.org/10.5281/zenodo.7160536Test
https://doi.org/10.5281/zenodo.7160538Test
https://doi.org/10.5281/zenodo.7160540Test
https://doi.org/10.5281/zenodo.7160542Test
https://doi.org/10.5281/zenodo.7160546Test
https://doi.org/10.5281/zenodo.7160548Test
https://doi.org/10.5281/zenodo.7160552Test
https://doi.org/10.1007/978-94-011-3102-5_6Test