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27 results on '"Abueg, Linelle"'

2. Chromosome level genome assembly of the Etruscan shrew Suncus etruscus

Author

Bukhman, Yury V., Meyer, Susanne, Chu, Li-Fang, Abueg, Linelle, Antosiewicz-Bourget, Jessica, Balacco, Jennifer, Brecht, Michael, Dinatale, Erica, Fedrigo, Olivier, Formenti, Giulio, Fungtammasan, Arkarachai, Giri, Swagarika Jaharlal, Hiller, Michael, Howe, Kerstin, Kihara, Daisuke, Mamott, Daniel, Mountcastle, Jacquelyn, Pelan, Sarah, Rabbani, Keon, Sims, Ying, Tracey, Alan, Wood, Jonathan M. D., Jarvis, Erich D., Thomson, James A., Chaisson, Mark J. P., and Stewart, Ron

Published
2024
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3. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Author

Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D., Rabbani, Keon, Antunes, Agostinho, Balacco, Jennifer R., Chaisson, Mark J. P., Cheng, Haoyu, Collins, Joanna, Couture, Melanie, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Horan, Kathleen, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O’Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Williams, Robert W., Waterhouse, Robert M., Phillippy, Adam M., Jarvis, Erich D., Schatz, Michael C., Nekrutenko, Anton, and Formenti, Giulio

Published
2024
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4. Bridging the gap in African biodiversity genomics and bioinformatics

Author

Sharaf, Abdoallah, Ndiribe, Charlotte C., Omotoriogun, Taiwo Crossby, Abueg, Linelle, Badaoui, Bouabid, Badiane Markey, Fatu J., Beedessee, Girish, Diouf, Diaga, Duru, Vincent C., Ebuzome, Chukwuike, Eziuzor, Samuel C., Jaufeerally Fakim, Yasmina, Formenti, Giulio, Ghanmi, Nidhal, Guerfali, Fatma Zahra, Houaga, Isidore, Ideozu, Justin Eze, Katee, Sally Mueni, Khayi, Slimane, Kuja, Josiah O., Kwon-Ndung, Emmanuel Hala, Marks, Rose A., Moila, Acclaim M., Mungloo-Dilmohamud, Zahra, Muzemil, Sadik, Nigussie, Helen, Osuji, Julian O., Ras, Verena, Tchiechoua, Yves H., Zoclanclounon, Yedomon Ange Bovys, Tolley, Krystal A., Ziyomo, Cathrine, Mapholi, Ntanganedzeni, Muigai, Anne W. T., Djikeng, Appolinaire, and Ebenezer, ThankGod Echezona

Published
2023
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7. A chromosome-level reference genome and pangenome for barn swallow population genomics

Author

Secomandi, Simona, Gallo, Guido R., Sozzoni, Marcella, Iannucci, Alessio, Galati, Elena, Abueg, Linelle, Balacco, Jennifer, Caprioli, Manuela, Chow, William, Ciofi, Claudio, Collins, Joanna, Fedrigo, Olivier, Ferretti, Luca, Fungtammasan, Arkarachai, Haase, Bettina, Howe, Kerstin, Kwak, Woori, Lombardo, Gianluca, Masterson, Patrick, Messina, Graziella, Møller, Anders P., Mountcastle, Jacquelyn, Mousseau, Timothy A., Ferrer Obiol, Joan, Olivieri, Anna, Rhie, Arang, Rubolini, Diego, Saclier, Marielle, Stanyon, Roscoe, Stucki, David, Thibaud-Nissen, Françoise, Torrance, James, Torroni, Antonio, Weber, Kristina, Ambrosini, Roberto, Bonisoli-Alquati, Andrea, Jarvis, Erich D., Gianfranceschi, Luca, and Formenti, Giulio

Published
2023
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8. A chromosome-level genome assembly for the dugong (Dugong dugon)

Author

Baker, Dorothy Nevé, primary, Abueg, Linelle, additional, Escalona, Merly, additional, Farquharson, Katherine A, additional, Lanyon, Janet M, additional, Le Duc, Diana, additional, Schöneberg, Torsten, additional, Absolon, Dominic, additional, Sims, Ying, additional, Fedrigo, Olivier, additional, Jarvis, Erich D, additional, Belov, Katherine, additional, Hogg, Carolyn J, additional, and Shapiro, Beth, additional

Published
2024
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9. A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments

Author

Cadena, Daniel, primary, Pabon, Laura, additional, DoNascimiento, Carlos, additional, Abueg, Linelle, additional, Tiley, Tatiana, additional, O-Toole, Brian, additional, Absolon, Dominic, additional, Sims, Ying, additional, Formenti, Giulio, additional, Fedrigo, Olivier, additional, Jarvis, Erich, additional, and Torres, Mauricio, additional

Published
2023
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10. Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761

Author

Skorupski, Jakub, primary, Brandes, Florian, additional, Seebass, Christian, additional, Festl, Wolfgang, additional, Śmietana, Przemysław, additional, Balacco, Jennifer, additional, Jain, Nivesh, additional, Tilley, Tatiana, additional, Abueg, Linelle, additional, Wood, Jonathan, additional, Sims, Ying, additional, Formenti, Giulio, additional, Fedrigo, Olivier, additional, and Jarvis, Erich D., additional

Published
2023
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11. A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): Building genomic resources to study evolution in cave environments.

Author

Cadena, Carlos Daniel, Pabón, Laura, DoNascimiento, Carlos, Abueg, Linelle, Tilley, Tatiana, O-Toole, Brian, Absolon, Dominic, Sims, Ying, Formenti, Giulio, Fedrigo, Olivier, Jarvis, Erich D, and Torres, Mauricio

Subjects
CATFISHES, EYE color, CAVES, CONVERGENT evolution, CAVE animals, DNA copy number variations
Abstract

Animals living in caves are of broad relevance to evolutionary biologists interested in understanding the mechanisms underpinning convergent evolution. In the Eastern Andes of Colombia, populations from at least two distinct clades of Trichomycterus catfishes (Siluriformes) independently colonized cave environments and converged in phenotype by losing their eyes and pigmentation. We are pursuing several research questions using genomics to understand the evolutionary forces and molecular mechanisms responsible for repeated morphological changes in this system. As a foundation for such studies, here we describe a diploid, chromosome-scale, long-read reference genome for Trichomycterus rosablanca , a blind, depigmented species endemic to the karstic system of the department of Santander. The nuclear genome comprises 1 Gb in 27 chromosomes, with a 40.0× HiFi long-read genome coverage having an N50 scaffold of 40.4 Mb and N50 contig of 13.1 Mb, with 96.9% (Eukaryota) and 95.4% (Actinopterygii) universal single-copy orthologs (BUSCO). This assembly provides the first reference genome for the speciose genus Trichomycterus , serving as a key resource for research on the genomics of phenotypic evolution. [ABSTRACT FROM AUTHOR]

Published
2024
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12. A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta)

Author

Squires, Theodore E., Rödin Mörch, Patrik, Formenti, Giulio, Tracey, Alan, Abueg, Linelle, Brajuka, Nadolina, Jarvis, Erich, Halapi, Eva C., Melsted, Pall, Höglund, Jacob, Magnusson, Kristinn Petur, Squires, Theodore E., Rödin Mörch, Patrik, Formenti, Giulio, Tracey, Alan, Abueg, Linelle, Brajuka, Nadolina, Jarvis, Erich, Halapi, Eva C., Melsted, Pall, Höglund, Jacob, and Magnusson, Kristinn Petur

Abstract

The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a highquality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes).

Published
2023
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13. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

Author

Larivière, Delphine, primary, Abueg, Linelle, additional, Brajuka, Nadolina, additional, Gallardo-Alba, Cristóbal, additional, Grüning, Bjorn, additional, Ko, Byung June, additional, Ostrovsky, Alex, additional, Palmada-Flores, Marc, additional, Pickett, Brandon D., additional, Rabbani, Keon, additional, Balacco, Jennifer R., additional, Chaisson, Mark, additional, Cheng, Haoyu, additional, Collins, Joanna, additional, Denisova, Alexandra, additional, Fedrigo, Olivier, additional, Gallo, Guido Roberto, additional, Giani, Alice Maria, additional, Gooder, Grenville MacDonald, additional, Jain, Nivesh, additional, Johnson, Cassidy, additional, Kim, Heebal, additional, Lee, Chul, additional, Marques-Bonet, Tomas, additional, O’Toole, Brian, additional, Rhie, Arang, additional, Secomandi, Simona, additional, Sozzoni, Marcella, additional, Tilley, Tatiana, additional, Uliano-Silva, Marcela, additional, van den Beek, Marius, additional, Waterhouse, Robert M., additional, Phillippy, Adam M., additional, Jarvis, Erich D., additional, Schatz, Michael C., additional, Nekrutenko, Anton, additional, and Formenti, Giulio, additional

Published
2023
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14. Open Institute of the African BioGenome Project: Bridging the gap in African biodiversity genomics and bioinformatics

Author

Sharaf, Abdoallah, primary, Ndiribe, Charlotte C., additional, Omotoriogun, Taiwo Crossby, additional, Abueg, Linelle, additional, Badaoui, Bouabid, additional, Markey, Fatu J. Badiane, additional, Beedesse, Girish, additional, Diouf, Diaga, additional, Duru, Vincent C., additional, Ebuzome, Chukwuike, additional, Eziuzor, Samuel C, additional, Fakim, asmina Jaufeerally, additional, Formenti, Giulio, additional, Ghanmi, Nidhal, additional, Guerfali, Fatma Zahra, additional, Houaga, Isidore, additional, Ideozu, Justin Eze, additional, Katee, Sally Mueni, additional, Khayi, Slimane, additional, Kuja, Josiah O., additional, Kwon-Ndung, Emmanuel Hala, additional, Marks, Rose A., additional, Moila, Acclaim M., additional, Mungloo-Dilmohamud, Zahra, additional, Muzemil, Sadik, additional, Negussie, Helen, additional, Osuji, Julian O., additional, Ras, Verena, additional, Tchiechoua, Yves H., additional, Zoclanclounon, Yedomon Ange Bovys, additional, Tolley, Krystal A., additional, Ziyomo, Cathrine, additional, Mapholi, Ntanganedzeni, additional, Muigai, Anne W.T., additional, Djikeng, Appolinaire, additional, and Ebenezer, ThankGod E., additional

Published
2023
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15. A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta)

Author

Squires, Theodore E, primary, Rödin-Mörch, Patrik, additional, Formenti, Giulio, additional, Tracey, Alan, additional, Abueg, Linelle, additional, Brajuka, Nadolina, additional, Jarvis, Erich, additional, Halapi, Eva C, additional, Melsted, Páll, additional, Höglund, Jacob, additional, and Magnússon, Kristinn Pétur, additional

Published
2023
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16. Open Institute of the African BioGenome Project: Bridging the gap in African biodiversity genomics and bioinformatics

Author

Sharaf, Abdoallah, Ndiribe, Charlotte C., Omotoriogun, Taiwo Crossby, Abueg, Linelle, Badaou, Bouabid, Markey, Fatu J. Badiane, Beedessee, Girish, Diouf, Diaga, Duru, Vincent C., Ebuzome, Chukwuike, Eziuzo, Samuel C., Jaufeerally Fakim, Yasmina, Formenti, Giulio, Ghanm, Nidhal, Guerfali, Fatma Zahra, Houaga, Isidore, Ideozu, Justin Eze, Katee, Sally Mueni, Khayi, Slimane, Kuja, Josiah O., Kwon-Ndung, Emmanuel Hala, Marks, Rose A., Moila, Acclaim M., Mungloo-Dilmohamud, Zahra, Muzemi, Sadik, Negussie, Helen, Osuji, Julian O., Ras, Verena, Tchiechoua, Yves H., Zoclanclounon, Yedomon Ange Bovys, Tolley, Krystal A., Ziyomo, Cathrine, Mapholi, Ntanganedzeni, Muigai, Anne, and Djikeng, Appolinaire

Abstract

Africa, a continent of 1.3 billion people, had 326 researchers per one million people in 2018 (Schneegans, 2021; UNESCO, 2022), despite the global average for the number of researchers per million people being 1368 (Schneegans, 2021; UNESCO, 2022). Nevertheless, a strong research community is a requirement to advance scientific knowledge and innovation and drive economic growth (Agnew, et al., 2020; Sianes, et al., 2022). This low number of researchers extends to scientific research across Africa and finds resonance with genomic projects such as the African BioGenome Project (Ebenezer, et al., 2022).The African BioGenome project (AfricaBP) plans to sequence 100,000 endemic African species in 10 years (Ebenezer, et al., 2022) with an estimated 203,000 gigabases of DNA sequence. AfricaBP aims to generate these genomes on-the-ground in Africa. However, for AfricaBP to achieve its goals of on-the-ground sequencing and data analysis, there is a need to empower African scientists and institutions to obtain the required skill sets, capacity and infrastructure to generate, analyse, and utilise these sequenced genomes in-country.The Open Institute is the genomics and bioinformatics knowledge exchange programme for the AfricaBP (Figures 1 & 2). It consists of 10 participating institutions including the University of South Africa in South Africa and National Institute of Agricultural Research in Morocco. It aims to: develop biodiversity genomics and bioinformatics curricula targeted at African scientists, promote and develop genomics and bioinformatics tools that will address critical needs relevant to the African terrain such as limited internet access, and advance grassroot knowledge exchange through outreach and public engagement such as quarterly training and workshops.

Published
2023
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17. Additional file 3 of MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Author

Uliano-Silva, Marcela, Ferreira, João Gabriel R. N., Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W., Durbin, Richard, Blaxter, Mark, and McCarthy, Shane A.

Abstract

Additional file 3. Figure 1. Dotplots of MitoHiFi mitogenomes (x axis) with their pre-existing mitogenome assemblies (y axis) for each species.

Published
2023
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18. Additional file 2 of MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Author

Uliano-Silva, Marcela, Ferreira, João Gabriel R. N., Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W., Durbin, Richard, Blaxter, Mark, and McCarthy, Shane A.

Abstract

Additional file 2. List of species that were assembled by MitoHiFi and that also had previous mitogenomes available on online databases.

Published
2023
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19. Additional file 4 of MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Author

Uliano-Silva, Marcela, Ferreira, João Gabriel R. N., Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W., Durbin, Richard, Blaxter, Mark, and McCarthy, Shane A.

Abstract

Additional file 4. Figure 2. Screenshots of IGV plots of reads mapped back to Andrea bucephala mitogenome before and after NUMTs reads were removed.

Published
2023
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20. A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta)

Author

Squires, Theodore E., primary, Rödin-Mörch, Patrik, additional, Formenti, Giulio, additional, Tracey, Alan, additional, Abueg, Linelle, additional, Brajuka, Nadolina, additional, Jarvis, Erich, additional, Halapi, Eva C., additional, Melsted, Páll, additional, Höglund, Jacob, additional, and Magnússon, Kristinn Pétur, additional

Published
2023
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22. Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Author

Secomandi, Simona, primary, Gallo, Guido Roberto, additional, Sozzoni, Marcella, additional, Iannucci, Alessio, additional, Galati, Elena, additional, Abueg, Linelle, additional, Balacco, Jennifer, additional, Caprioli, Manuela, additional, Chow, William, additional, Ciofi, Claudio, additional, Collins, Joanna, additional, Fedrigo, Olivier, additional, Ferretti, Luca, additional, Fungtammasan, Arkarachai, additional, Haase, Bettina, additional, Howe, Kerstin, additional, Kwak, Woori, additional, Lombardo, Gianluca, additional, Masterson, Patrick, additional, Messina, Graziella, additional, Møller, Anders Pape, additional, Mountcastle, Jacquelyn, additional, Mousseau, Timothy A., additional, Ferrer-Obiol, Joan, additional, Olivieri, Anna, additional, Rhie, Arang, additional, Rubolini, Diego, additional, Saclier, Marielle, additional, Stanyon, Roscoe, additional, Stucki, David, additional, Thibaud-Nissen, Françoise, additional, Torrance, James, additional, Torroni, Antonio, additional, Weber, Kristina, additional, Ambrosini, Roberto, additional, Bonisoli-Alquati, Andrea, additional, Jarvis, Erich D., additional, Gianfranceschi, Luca, additional, and Formenti, Giulio, additional

Published
2022
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24. Landscape Genomics of White-Footed Mice (Peromyscus leucopus) along an Urban-to-Rural Gradient in the New York City Metropolitan Area

Author

Abueg, Linelle Ann Lacson and Abueg, Linelle Ann Lacson

Abstract

Urbanization can change an area’s habitat in ways that pose novel selection pressures on native species, and previous work has shown evidence for divergent selection in white-footed mice populations in New York City (NYC) parks compared to nearby rural populations. This study aims to 1) identify potential candidate genes exhibiting signatures of selection with increasing levels of urbanization, and 2) compare these results with previous findings that NYC populations of P. leucopus experience directional selection for metabolic processes and immune function. I approached these aims using a SNP dataset derived from exomes of 95 P. leucopus specimens sampled from sites in and around NYC. Outlier detection consisted of methods which rely on measures of population genetics (such as FST) and genotype-environment analyses that incorporate environmental factors (such as degree of urbanization). I ran Gene Ontology enrichment tests on the resulting outliers to see what biological functions are overrepresented among the outliers. I found overrepresentation of genes related to metabolic function as well as ciliary function, particularly with regard to spermatogenesis, which corroborates previous findings in this system. I additionally found multiple unconventional myosins and other proteins that imply possible selection on genes related to hearing function.

Published
2019

25. The genome sequence of Molossus alvarezi González-Ruiz, Ramírez-Pulido and Arroyo-Cabrales, 2011 (Chiroptera, Molossidae).

Author

Simmons NB, Ingala MR, Pieri M, O'Toole BP, Gray JL, Philge P, L Volkert T, Zhang N, Abueg L, Brajuka N, Jarvis E, Formenti G, McCaffrey K, Mai M, Teeling EC, and C Vernes S

Abstract

We present a genome assembly from an individual female Molossus alvarezi (Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.490 Gb in span. The majority of the assembly is scaffolded into 24 chromosomal pseudomolecules, with the X sex chromosomes assembled., Competing Interests: Competing interests: BPO, JLG and NZ TLV are employees of Paratus Sciences Corporation and are option holders. PP serves as a consultant for Paratus Sciences Corporation. NBS, MP, TLV, LA, NB, EJ, GF, KM, MM, ECT and SCV declare no competing interests., (Copyright: © 2024 Simmons NB et al.)

Published
2024
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26. The genome sequence of Rhynchonycteris naso, Peters, 1867 (Chiroptera, Emballonuridae, Rhynchonycteris).

Author

Alvarez van Tussenbroek I, Knörnschild M, Nagy M, O'Toole BP, Formenti G, Philge P, Zhang N, Abueg L, Brajuka N, Jarvis E, Volkert TL, Gray JL, Pieri M, Mai M, Teeling EC, and Vernes SC

Abstract

We present a reference genome assembly from an individual male Rhynchonycteris naso (Chordata; Mammalia; Chiroptera; Emballonuridae). The genome sequence is 2.46 Gb in span. The majority of the assembly is scaffolded into 22 chromosomal pseudomolecules, with the Y sex chromosome assembled., Competing Interests: Competing interests: NZ and BPO are employees of Paratus Sciences Corporation and are option holders. PP serves as consultant for Paratus Sciences Corporation. IAVT, MK, MN, GF,LA, NB, EJ, VT, JLG, MP, MM, ECT and SCV declare no competing interests., (Copyright: © 2024 Alvarez van Tussenbroek I et al.)

Published
2024
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27. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.

Author

Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, and Formenti G

Abstract

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

Published
2023
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