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1. Purposive breeding strategies drive genetic differentiation in Thai fighting cock breeds

Author

Budi, Trifan, Luu, Anh Huynh, Singchat, Worapong, Wongloet, Wongsathit, Rey, Juniman, Kumnan, Nichakorn, Chalermwong, Piangjai, Nguyen, Chien Phuoc Tran, Panthum, Thitipong, Tanglertpaibul, Nivit, Thong, Thanyapat, Ali, Hina, Vangnai, Kanithaporn, Chaiyes, Aingorn, Yokthongwattana, Chotika, Sinthuvanich, Chomdao, Han, Kyudong, Antunes, Agostinho, Muangmai, Narongrit, Duengkae, Prateep, and Srikulnath, Kornsorn

Published
2024
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2. Complexity of avian evolution revealed by family-level genomes

Author

Stiller, Josefin, Feng, Shaohong, Chowdhury, Al-Aabid, Rivas-González, Iker, Duchêne, David A., Fang, Qi, Deng, Yuan, Kozlov, Alexey, Stamatakis, Alexandros, Claramunt, Santiago, Nguyen, Jacqueline M. T., Ho, Simon Y. W., Faircloth, Brant C., Haag, Julia, Houde, Peter, Cracraft, Joel, Balaban, Metin, Mai, Uyen, Chen, Guangji, Gao, Rongsheng, Zhou, Chengran, Xie, Yulong, Huang, Zijian, Cao, Zhen, Yan, Zhi, Ogilvie, Huw A., Nakhleh, Luay, Lindow, Bent, Morel, Benoit, Fjeldså, Jon, Hosner, Peter A., da Fonseca, Rute R., Petersen, Bent, Tobias, Joseph A., Székely, Tamás, Kennedy, Jonathan David, Reeve, Andrew Hart, Liker, Andras, Stervander, Martin, Antunes, Agostinho, Tietze, Dieter Thomas, Bertelsen, Mads F., Lei, Fumin, Rahbek, Carsten, Graves, Gary R., Schierup, Mikkel H., Warnow, Tandy, Braun, Edward L., Gilbert, M. Thomas P., Jarvis, Erich D., Mirarab, Siavash, and Zhang, Guojie

Published
2024
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3. Building a Portuguese coalition for biodiversity genomics

Author

Marques, João P., Alves, Paulo C., Amorim, Isabel R., Lopes, Ricardo J., Moura, Monica, Myers, Eugene, Sim-sim, Manuela, Sousa-Santos, Carla, Alves, M. Judite, Borges, Paulo A. V., Brown, Thomas, Carneiro, Miguel, Carrapato, Carlos, Ceríaco, Luís M. P., Ciofi, Claúdio, da Silva, Luís P., Diedericks, Genevieve, Diroma, Maria Angela, Farelo, Liliana, Formenti, Giulio, Gil, Fátima, Grilo, Miguel, Iannucci, Alessio, Leitão, Henrique G., Máguas, Cristina, Mc Cartney, Ann M., Mendes, Sofia L., Moreno, João M., Morselli, Marco, Mouton, Alice, Natali, Chiara, Pereira, Fernando, Rego, Rúben M. C., Resendes, Roberto, Roxo, Guilherme, Svardal, Hannes, Trindade, Helena, Vicente, Sara, Winkler, Sylke, Alvarenga, Marcela, Amaral, Andreia J., Antunes, Agostinho, Campos, Paula F., Canário, Adelino V. M., Castilho, Rita, Castro, L. Filipe C., Crottini, Angelica, Cunha, Mónica V., Espregueira Themudo, Gonçalo, Esteves, Pedro J., Faria, Rui, Rodríguez Fernandes, Carlos, Ledoux, Jean-Baptiste, Louro, Bruno, Magalhaes, Sara, Paulo, Octávio S., Pearson, Gareth, Pimenta, João, Pina-Martins, Francisco, Santos, Teresa L., Serrão, Ester, Melo-Ferreira, José, and Sousa, Vítor C.

Published
2024
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6. 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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7. Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

Author

Jaito, Wattanawan, Sonongbua, Jumaporn, Panthum, Thitipong, Wattanadilokcahtkun, Pish, Ariyaraphong, Nattakan, Thong, Thanyapat, Singchat, Worapong, Ahmad, Syed Farhan, Kraichak, Ekaphan, Muangmai, Narongrit, Han, Kyudong, Antunes, Agostinho, Sitdhibutr, Ratiwan, Koga, Akihiko, Duengkae, Prateep, Kasorndorkbua, Chaiyan, and Srikulnath, Kornsorn

Published
2024
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8. Genome-wide sequence divergence of satellite DNA could underlie meiotic failure in male hybrids of bighead catfish and North African catfish (Clarias, Clariidae)

Author

Lisachov, Artem, Panthum, Thitipong, Dedukh, Dmitrij, Singchat, Worapong, Ahmad, Syed Farhan, Wattanadilokcahtkun, Pish, Thong, Thanyapat, Srikampa, Phanitada, Noito, Kantika, Rasoarahona, Ryan, Kraichak, Ekaphan, Muangmai, Narongrit, Chatchaiphan, Satid, Sriphairoj, Kednapat, Hatachote, Sittichai, Chaiyes, Aingorn, Jantasuriyarat, Chatchawan, Dokkaew, Sahabhop, Chailertlit, Visarut, Suksavate, Warong, Sonongbua, Jumaporn, Prasanpan, Jiraboon, Payungporn, Sunchai, Han, Kyudong, Antunes, Agostinho, Srisapoome, Prapansak, Koga, Akihiko, Duengkae, Prateep, Na-Nakorn, Uthairat, Matsuda, Yoichi, and Srikulnath, Kornsorn

Published
2024
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10. MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes

Author

Rasoarahona, Ryan, Wattanadilokchatkun, Pish, Panthum, Thitipong, Jaisamut, Kitipong, Lisachov, Artem, Thong, Thanyapat, Singchat, Worapong, Ahmad, Syed Farhan, Han, Kyudong, Kraichak, Ekaphan, Muangmai, Narongrit, Koga, Akihiko, Duengkae, Prateep, Antunes, Agostinho, and Srikulnath, Kornsorn

Published
2023
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11. Vendors’ perceptions on the bushmeat trade dynamics across West and central Africa during the COVID-19 pandemic: Lessons learned on sanitary measures and awareness campaigns

Author

Gaubert, Philippe, Djagoun, Chabi A.M.S., Missoup, Alain Didier, Ales, Nazif, Amougou, Claude Vianney, Dipita, Alain Din, Djagoun, Joël, Gossé, Koffi Jules, Koffi, Cécilia Espérence, N’Goran, Edwidge Michèle, Noma, Yves Noma, Zanvo, Stanislas, Tindo, Maurice, Antunes, Agostinho, and Gonedelé-Bi, Sery

Published
2024
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14. A draft genome sequence of the elusive giant squid, Architeuthis dux

Author

da Fonseca, Rute R, Couto, Alvarina, Machado, Andre M, Brejova, Brona, Albertin, Carolin B, Silva, Filipe, Gardner, Paul, Baril, Tobias, Hayward, Alex, Campos, Alexandre, Ribeiro, Ângela M, Barrio-Hernandez, Inigo, Hoving, Henk-Jan, Tafur-Jimenez, Ricardo, Chu, Chong, Frazão, Barbara, Petersen, Bent, Peñaloza, Fernando, Musacchia, Francesco, Alexander, Graham C, Osório, Hugo, Winkelmann, Inger, Simakov, Oleg, Rasmussen, Simon, Rahman, M Ziaur, Pisani, Davide, Vinther, Jakob, Jarvis, Erich, Zhang, Guojie, Strugnell, Jan M, Castro, L Filipe C, Fedrigo, Olivier, Patricio, Mateus, Li, Qiye, Rocha, Sara, Antunes, Agostinho, Wu, Yufeng, Ma, Bin, Sanges, Remo, Vinar, Tomas, Blagoev, Blagoy, Sicheritz-Ponten, Thomas, Nielsen, Rasmus, and Gilbert, M Thomas P

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Life Below Water, Animals, Biological Evolution, Chromatography, Liquid, Computational Biology, DNA Transposable Elements, Decapodiformes, Gene Expression Profiling, Genome, Genomics, Molecular Sequence Annotation, Multigene Family, RNA, Untranslated, Tandem Mass Spectrometry, Transcriptome, Whole Genome Sequencing, cephalopod, invertebrate, genome assembly
Abstract

BackgroundThe giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.FindingsWe present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.ConclusionsThis annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Published
2020

17. The era of reference genomes in conservation genomics

Author

Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.

Published
2022
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18. Innovative Alignment-Based Method for Antiviral Peptide Prediction.

Author

de Llano García, Daniela, Marrero-Ponce, Yovani, Agüero-Chapin, Guillermin, Ferri, Francesc J., Antunes, Agostinho, Martinez-Rios, Felix, and Rodríguez, Hortensia

Subjects
PEPTIDES, DEEP learning, MACHINE learning, DRUG resistance, VIRUS diseases
Abstract

Antiviral peptides (AVPs) represent a promising strategy for addressing the global challenges of viral infections and their growing resistances to traditional drugs. Lab-based AVP discovery methods are resource-intensive, highlighting the need for efficient computational alternatives. In this study, we developed five non-trained but supervised multi-query similarity search models (MQSSMs) integrated into the StarPep toolbox. Rigorous testing and validation across diverse AVP datasets confirmed the models' robustness and reliability. The top-performing model, M13+, demonstrated impressive results, with an accuracy of 0.969 and a Matthew's correlation coefficient of 0.71. To assess their competitiveness, the top five models were benchmarked against 14 publicly available machine-learning and deep-learning AVP predictors. The MQSSMs outperformed these predictors, highlighting their efficiency in terms of resource demand and public accessibility. Another significant achievement of this study is the creation of the most comprehensive dataset of antiviral sequences to date. In general, these results suggest that MQSSMs are promissory tools to develop good alignment-based models that can be successfully applied in the screening of large datasets for new AVP discovery. [ABSTRACT FROM AUTHOR]

Published
2024
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21. A region of suppressed recombination misleads neoavian phylogenomics

Author

Mirarab, Siavash, primary, Rivas-González, Iker, additional, Feng, Shaohong, additional, Stiller, Josefin, additional, Fang, Qi, additional, Mai, Uyen, additional, Hickey, Glenn, additional, Chen, Guangji, additional, Brajuka, Nadolina, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Wolf, Jochen B. W., additional, Howe, Kerstin, additional, Antunes, Agostinho, additional, Schierup, Mikkel H., additional, Paten, Benedict, additional, Jarvis, Erich D., additional, Zhang, Guojie, additional, and Braun, Edward L., additional

Published
2024
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24. The evolutionary history of extinct and living lions

Author

de Manuel, Marc, Barnett, Ross, Sandoval-Velasco, Marcela, Yamaguchi, Nobuyuki, Vieira, Filipe Garrett, Mendoza, M. Lisandra Zepeda, Liu, Shiping, Martin, Michael D., Sinding, Mikkel-Holger S., Mak, Sarah S. T., Carøe, Christian, Liu, Shanlin, Guo, Chunxue, Zheng, Jiao, Zazula, Grant, Baryshnikov, Gennady, Eizirik, Eduardo, Koepfli, Klaus-Peter, Johnson, Warren E., Antunes, Agostinho, Sicheritz-Ponten, Thomas, Gopalakrishnan, Shyam, Larson, Greger, Yang, Huanming, O’Brien, Stephen J., Hansen, Anders J., Zhang, Guojie, Marques-Bonet, Tomas, and Gilbert, M. Thomas P.

Published
2020

25. Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

Author

Figueiró, Henrique V, Li, Gang, Trindade, Fernanda J, Assis, Juliana, Pais, Fabiano, Fernandes, Gabriel, Santos, Sarah HD, Hughes, Graham M, Komissarov, Aleksey, Antunes, Agostinho, Trinca, Cristine S, Rodrigues, Maíra R, Linderoth, Tyler, Bi, Ke, Silveira, Leandro, Azevedo, Fernando CC, Kantek, Daniel, Ramalho, Emiliano, Brassaloti, Ricardo A, Villela, Priscilla MS, Nunes, Adauto LV, Teixeira, Rodrigo HF, Morato, Ronaldo G, Loska, Damian, Saragüeta, Patricia, Gabaldón, Toni, Teeling, Emma C, O'Brien, Stephen J, Nielsen, Rasmus, Coutinho, Luiz L, Oliveira, Guilherme, Murphy, William J, and Eizirik, Eduardo

Subjects
Animals, Panthera, Computational Biology, Genomics, Evolution, Molecular, Phylogeny, Genome, Genetic Variation, Genome-Wide Association Study, Selection, Genetic, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing, Evolution, Molecular, Selection, Genetic
Abstract

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.

Published
2017

28. A region of suppressed recombination misleads neoavian phylogenomics

Author

Mirarab, Siavash, Rivas-González, Iker, Feng, Shaohong, Stiller, Josefin, Fang, Qi, Mai, Uyen, Hickey, Glenn, Chen, Guangji, Brajuka, Nadolina, Fedrigo, Olivier, Formenti, Giulio, Wolf, Jochen B. W., Howe, Kerstin, Antunes, Agostinho, Schierup, Mikkel H., Paten, Benedict, Jarvis, Erich D., Zhang, Guojie, Braun, Edward L., Mirarab, Siavash, Rivas-González, Iker, Feng, Shaohong, Stiller, Josefin, Fang, Qi, Mai, Uyen, Hickey, Glenn, Chen, Guangji, Brajuka, Nadolina, Fedrigo, Olivier, Formenti, Giulio, Wolf, Jochen B. W., Howe, Kerstin, Antunes, Agostinho, Schierup, Mikkel H., Paten, Benedict, Jarvis, Erich D., Zhang, Guojie, and Braun, Edward L.

Abstract

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

Published
2024

34. Genome-Wide Sequence Divergence of Satellite DNA Could Underlie Meiotic Failure in Male Hybrids of Bighead Catfish and North African Catfish (Clarias, Clariidae)

Author

Lunev, Anton, primary, Panthum, Thitipong, additional, Dedukh, Dmitrij, additional, Singchat, Worapong, additional, Ahmad, Syed Farhan, additional, Wattanadilokchatkun, Pish, additional, Thong, Thanyapat, additional, Srikampa, Phanitada, additional, Noito, Kantika, additional, Rasoarahona, Ryan, additional, Kraichak, Ekaphan, additional, Muangmai, Narongrit, additional, Chatchaiphan, Satid, additional, Sriphairoj, Kednapat, additional, Hatachote, Sittichai, additional, Chaiyes, Aingorn, additional, Jantasuriyarat, Chatchawan, additional, Dokkaew, Sahabhop, additional, Chailertlit, Visarut, additional, Suksavate, Warong, additional, Sonongbua, Jumaporn, additional, Prasanpan, Jiraboon, additional, Payungporn, Sunchai, additional, Han, Kyudong, additional, Antunes, Agostinho, additional, Srisapoome, Prapansak, additional, Koga, Akihiko, additional, Duengkae, Prateep, additional, Na-Nakorn, Uthairat, additional, Matsuda, Yoichi, additional, and Srikulnath, Kornsorn, additional

Published
2024
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38. Comparative genomics reveals insights into avian genome evolution and adaptation

Author

Zhang, Guojie, Li, Cai, Li, Qiye, Li, Bo, Larkin, Denis M, Lee, Chul, Storz, Jay F, Antunes, Agostinho, Greenwold, Matthew J, Meredith, Robert W, Ödeen, Anders, Cui, Jie, Zhou, Qi, Xu, Luohao, Pan, Hailin, Wang, Zongji, Jin, Lijun, Zhang, Pei, Hu, Haofu, Yang, Wei, Hu, Jiang, Xiao, Jin, Yang, Zhikai, Liu, Yang, Xie, Qiaolin, Yu, Hao, Lian, Jinmin, Wen, Ping, Zhang, Fang, Li, Hui, Zeng, Yongli, Xiong, Zijun, Liu, Shiping, Zhou, Long, Huang, Zhiyong, An, Na, Wang, Jie, Zheng, Qiumei, Xiong, Yingqi, Wang, Guangbiao, Wang, Bo, Wang, Jingjing, Fan, Yu, da Fonseca, Rute R, Alfaro-Núñez, Alonzo, Schubert, Mikkel, Orlando, Ludovic, Mourier, Tobias, Howard, Jason T, Ganapathy, Ganeshkumar, Pfenning, Andreas, Whitney, Osceola, Rivas, Miriam V, Hara, Erina, Smith, Julia, Farré, Marta, Narayan, Jitendra, Slavov, Gancho, Romanov, Michael N, Borges, Rui, Machado, João Paulo, Khan, Imran, Springer, Mark S, Gatesy, John, Hoffmann, Federico G, Opazo, Juan C, Håstad, Olle, Sawyer, Roger H, Kim, Heebal, Kim, Kyu-Won, Kim, Hyeon Jeong, Cho, Seoae, Li, Ning, Huang, Yinhua, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Bertelsen, Mads F, Derryberry, Elizabeth, Warren, Wesley, Wilson, Richard K, Li, Shengbin, Ray, David A, Green, Richard E, O’Brien, Stephen J, Griffin, Darren, Johnson, Warren E, Haussler, David, Ryder, Oliver A, Willerslev, Eske, Graves, Gary R, Alström, Per, Fjeldså, Jon, Mindell, David P, Edwards, Scott V, Braun, Edward L, Rahbek, Carsten, Burt, David W, Houde, Peter, and Zhang, Yong

Subjects
Human Genome, Biotechnology, Genetics, Adaptation, Physiological, Animals, Biodiversity, Biological Evolution, Birds, Conserved Sequence, Diet, Evolution, Molecular, Female, Flight, Animal, Genes, Genetic Variation, Genome, Genomics, Male, Molecular Sequence Annotation, Phylogeny, Reproduction, Selection, Genetic, Sequence Analysis, DNA, Synteny, Vision, Ocular, Vocalization, Animal, Avian Genome Consortium, General Science & Technology
Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Published
2014

40. Comparative population genetics of habitat-forming octocorals in two marine protected areas: eco-evolutionary and management implications

Author

Horaud, Mathilde, primary, Arizmendi-Meija, Rosana, additional, Nebot-Colomer, Elisabet, additional, López-Sendino, Paula, additional, Antunes, Agostinho, additional, Dellicour, Simon, additional, Viard, Frédérique, additional, Leblois, Raphael, additional, Linares, Cristina, additional, Garrabou, Joaquim, additional, and Ledoux, Jean-Baptiste, additional

Published
2023
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41. Overcoming taxonomic challenges in DNA barcoding for improvement of identification and preservation of clariid catfish species

Author

Chalermwong, Piangjai, primary, Panthum, Thitipong, additional, Wattanadilokcahtkun, Pish, additional, Ariyaraphong, Nattakan, additional, Thong, Thanyapat, additional, Srikampa, Phanitada, additional, Singchat, Worapong, additional, Ahmad, Syed Farhan, additional, Noito, Kantika, additional, Rasoarahona, Ryan, additional, Lisachov, Artem, additional, Ali, Hina, additional, Kraichak, Ekaphan, additional, Muangmai, Narongrit, additional, Chatchaiphan, Satid, additional, Sriphairoj, Kednapat, additional, Hatachote, Sittichai, additional, Chaiyes, Aingorn, additional, Jantasuriyarat, Chatchawan, additional, Chailertlit, Visarut, additional, Suksavate, Warong, additional, Sonongbua, Jumaporn, additional, Srimai, Witsanu, additional, Payungporn, Sunchai, additional, Han, Kyudong, additional, Antunes, Agostinho, additional, Srisapoome, Prapansak, additional, Koga, Akihiko, additional, Duengkae, Prateep, additional, Matsuda, Yoichi, additional, Na-Nakorn, Uthairat, additional, and Srikulnath, Kornsorn, additional

Published
2023
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42. In Silico Chromosome Mapping of the Male-Specific/Linked Loci in the Jade Perch (Scortum barcoo) Suggests Chromosome 19 as the Putative Y Sex Chromosome

Author

Panthum, Thitipong, primary, Wattanadilokchatkun, Pish, additional, Jaisamut, Kitipong, additional, Singchat, Worapong, additional, Ahmad, Syed Farhan, additional, Muangmai, Narongrit, additional, Duengkae, Prateep, additional, Antunes, Agostinho, additional, and Srikulnath, Kornsorn, additional

Published
2023
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43. Optimizing Microsatellite Marker Panels for Genetic Diversity and Population Genetic Studies: An Ant Colony Algorithm Approach with Polymorphic Information Content

Author

Rasoarahona, Ryan, primary, Wattanadilokchatkun, Pish, additional, Panthum, Thitipong, additional, Thong, Thanyapat, additional, Singchat, Worapong, additional, Ahmad, Syed Farhan, additional, Chaiyes, Aingorn, additional, Han, Kyudong, additional, Kraichak, Ekaphan, additional, Muangmai, Narongrit, additional, Koga, Akihiko, additional, Duengkae, Prateep, additional, Antunes, Agostinho, additional, and Srikulnath, Kornsorn, additional

Published
2023
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45. Contributors

Author

Acién-Fernández, Francisco Gabriel, primary, Ahmadzadeh, Hossein, additional, Alcántara, Cynthia, additional, Almeida, Allan Victor Martins, additional, Antunes, Agostinho, additional, Arakawa, Osamu, additional, Araújo, Wagner L., additional, Arora, Neha, additional, Asakawa, Manabu, additional, Barriada, Jose L., additional, Barsanti, Laura, additional, Bécares, Eloy, additional, Blanco, Saúl, additional, Blanfuné, Aurélie, additional, Bolado, Silvia, additional, Boudouresque, Charles F., additional, Canan, Cristiane, additional, Castro, Naira Valle de, additional, Cepoi, Liliana, additional, Chikkaputtaiah, Channakeshavaiah, additional, Christy, Ann D., additional, Colla, Eliane, additional, Costa, Jorge Alberto Vieira, additional, da Silva-Buzanello, Rosana Aparecida, additional, Daigo, Kinue, additional, Dalu, Tatenda, additional, Dawes, Clinton J., additional, Deka, Deepi, additional, Drunkler, Deisy Alessandra, additional, Esterhuizen-Londt, Maranda, additional, Fanka, Letícia Schneider, additional, Faraloni, Cecilia, additional, Fernández-Sevilla, José María, additional, García-Encina, Pedro, additional, García-González, María Cruz, additional, Goss, Reimund, additional, Gualtieri, Paolo, additional, Hernández, David, additional, Herrero, Roberto, additional, Irusta, Rubén, additional, Jaiswal, Damini, additional, Jakob, Torsten, additional, Kalschne, Daneysa Lahis, additional, Konur, Ozcan, additional, Kosinski, Roberta da Costa, additional, Larrán, Ana, additional, Lemley, Daniel A., additional, Lodeiro, Pablo, additional, Lyon, Stephen, additional, Makareviciene, Violeta, additional, Markou, Giorgos, additional, Martins, Joana, additional, Mathieson, Arthur C., additional, Matsuyama, Yukihiko, additional, Menegotto, Anne Luize Lupatini, additional, Metcalf, J.S., additional, Miyazawa, Keisuke, additional, Molazadeh, Marziyeh, additional, Morais, Michele Greque de, additional, Moreira, Cristiana, additional, Moreira, Juliana Botelho, additional, Muñoz, Raúl, additional, Noguchi, Tamao, additional, Nowruzi, Bahareh, additional, Nunes-Nesi, Adriano, additional, O’Neill, Ellis, additional, Oda, Tatsuya, additional, Oikawa, Hiroshi, additional, Ortíz, Sheyla, additional, Pflugmacher, Stephan, additional, Qin, Yimin, additional, Riaño, Berta, additional, Rodriguez-Barro, Pilar, additional, Ruitton, Sandrine, additional, Saba, Beenish, additional, Sarvari, Gisoo, additional, Sastre de Vicente, Manuel E., additional, Sendzikiene, Egle, additional, Sengupta, Shinjinee, additional, Shourian, Mostafa, additional, Snow, Gavin C., additional, Sonowal, Shashanka, additional, Souza, N.R., additional, Thibaut, Thierry, additional, Tomás, Cristina, additional, Torzillo, Giuseppe, additional, Vasconcelos, Vitor, additional, Vaz, Marcelo Gomes Marçal Vieira, additional, Velmurugan, Natarajan, additional, Vilariño, Teresa, additional, Wangikar, Pramod P., additional, Wilhelm, Christian, additional, Wu, Naicheng, additional, Zinicovscaia, Inga, additional, Znad, Hussein, additional, and Zohoorian, Hamidreza, additional

Published
2020
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49. How genomics can help biodiversity conservation

Author

Theissinger, Kathrin, primary, Fernandes, Carlos, additional, Formenti, Giulio, additional, Bista, Iliana, additional, Berg, Paul R., additional, Bleidorn, Christoph, additional, Bombarely, Aureliano, additional, Crottini, Angelica, additional, Gallo, Guido R., additional, Godoy, José A., additional, Jentoft, Sissel, additional, Malukiewicz, Joanna, additional, Mouton, Alice, additional, Oomen, Rebekah A., additional, Paez, Sadye, additional, Palsbøll, Per J., additional, Pampoulie, Christophe, additional, Ruiz-López, María J., additional, Secomandi, Simona, additional, Svardal, Hannes, additional, Theofanopoulou, Constantina, additional, de Vries, Jan, additional, Waldvogel, Ann-Marie, additional, Zhang, Guojie, additional, Jarvis, Erich D., additional, Bálint, Miklós, additional, Ciofi, Claudio, additional, Waterhouse, Robert M., additional, Mazzoni, Camila J., additional, Höglund, Jacob, additional, Aghayan, Sargis A., additional, Alioto, Tyler S., additional, Almudi, Isabel, additional, Alvarez, Nadir, additional, Alves, Paulo C., additional, Amorim do Rosario, Isabel R., additional, Antunes, Agostinho, additional, Arribas, Paula, additional, Baldrian, Petr, additional, Bertorelle, Giorgio, additional, Böhne, Astrid, additional, Bonisoli-Alquati, Andrea, additional, Boštjančić, Ljudevit L., additional, Boussau, Bastien, additional, Breton, Catherine M., additional, Buzan, Elena, additional, Campos, Paula F., additional, Carreras, Carlos, additional, Castro, L. FIlipe C., additional, Chueca, Luis J., additional, Čiampor, Fedor, additional, Conti, Elena, additional, Cook-Deegan, Robert, additional, Croll, Daniel, additional, Cunha, Mónica V., additional, Delsuc, Frédéric, additional, Dennis, Alice B., additional, Dimitrov, Dimitar, additional, Faria, Rui, additional, Favre, Adrien, additional, Fedrigo, Olivier D., additional, Fernández, Rosa, additional, Ficetola, Gentile Francesco, additional, Flot, Jean-François, additional, Gabaldón, Toni, additional, Agius, Dolores R., additional, Giani, Alice M., additional, Gilbert, M. Thomas P., additional, Grebenc, Tine, additional, Guschanski, Katerina, additional, Guyot, Romain, additional, Hausdorf, Bernhard, additional, Hawlitschek, Oliver, additional, Heintzman, Peter D., additional, Heinze, Berthold, additional, Hiller, Michael, additional, Husemann, Martin, additional, Iannucci, Alessio, additional, Irisarri, Iker, additional, Jakobsen, Kjetill S., additional, Klinga, Peter, additional, Kloch, Agnieszka, additional, Kratochwil, Claudius F., additional, Kusche, Henrik, additional, Layton, Kara K.S., additional, Leonard, Jennifer A., additional, Lerat, Emmanuelle, additional, Liti, Gianni, additional, Manousaki, Tereza, additional, Marques-Bonet, Tomas, additional, Matos-Maraví, Pável, additional, Matschiner, Michael, additional, Maumus, Florian, additional, Mc Cartney, Ann M., additional, Meiri, Shai, additional, Melo-Ferreira, José, additional, Mengual, Ximo, additional, Monaghan, Michael T., additional, Montagna, Matteo, additional, Mysłajek, Robert W., additional, Neiber, Marco T., additional, Nicolas, Violaine, additional, Novo, Marta, additional, Ozretić, Petar, additional, Palero, Ferran, additional, Pârvulescu, Lucian, additional, Pascual, Marta, additional, Paulo, Octávio S., additional, Pavlek, Martina, additional, Pegueroles, Cinta, additional, Pellissier, Loïc, additional, Pesole, Graziano, additional, Primmer, Craig R., additional, Riesgo, Ana, additional, Rüber, Lukas, additional, Rubolini, Diego, additional, Salvi, Daniele, additional, Seehausen, Ole, additional, Seidel, Matthias, additional, Studer, Bruno, additional, Theodoridis, Spyros, additional, Thines, Marco, additional, Urban, Lara, additional, Vasemägi, Anti, additional, Vella, Adriana, additional, Vella, Noel, additional, Vernes, Sonja C., additional, Vernesi, Cristiano, additional, Vieites, David R., additional, Wheat, Christopher W., additional, Wörheide, Gert, additional, Wurm, Yannick, additional, and Zammit, Gabrielle, additional

Published
2023
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