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4. Early Diversification of Membrane Intrinsic Proteins (MIPs) in Eukaryotes.

Author

Irisarri, Iker, Lorente-Martínez, Héctor, Strassert, Jürgen F H, Agorreta, Ainhoa, Zardoya, Rafael, Mauro, Diego San, and Vries, Jan de

Abstract

Membrane intrinsic proteins (MIPs), including aquaporins (AQPs) and aquaglyceroporins (GLPs), form an ancient family of transporters for water and small solutes across biological membranes. The evolutionary history and functions of MIPs have been extensively studied in vertebrates and land plants, but their widespread presence across the eukaryotic tree of life suggests both a more complex evolutionary history and a broader set of functions than previously thought. That said, the early evolution of MIPs remains obscure. The presence of one GLP and four AQP clades across both bacteria and archaea suggests that the first eukaryotes could have possessed up to five MIPs. Here, we report on a previously unknown richness in MIP diversity across all major eukaryotic lineages, including unicellular eukaryotes, which make up the bulk of eukaryotic diversity. Three MIP clades have likely deep evolutionary origins, dating back to the last eukaryotic common ancestor (LECA), and support the presence of a complex MIP repertoire in early eukaryotes. Overall, our findings highlight the growing complexity of the reconstructed LECA genome: the dynamic evolutionary history of MIPs was set in motion when eukaryotes were in their infancy followed by radiative bursts across all main eukaryotic lineages. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Phylogeny and origin of diversification of Amblyomma (Acari: Ixodidae)

Author

Uribe, Juan E., primary, Kelava, Samuel, additional, Nava, Santiago, additional, Cotes-Perdomo, Andrea P., additional, Castro, Lyda R., additional, Rivera-Paéz, Fredy A., additional, Perea, Silvia, additional, Mans, Ben J., additional, Gofton, Alexander, additional, Teo, Ernest J. M., additional, Zardoya, Rafael, additional, and Barker, Stephen C., additional

Published
2023
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19. Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes

Author

Abascal, Federico, Posada, David, Knight, Robin D, and Zardoya, Rafael

Subjects
Genetics, Animals, Arthropods, Codon, Computer Simulation, DNA, Mitochondrial, Evolution, Molecular, Genes, Mitochondrial, Genetic Code, Models, Genetic, Phylogeny, RNA, Transfer, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code). We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments.

Published
2006

20. Multiple Instances of Adaptive Evolution in Aquaporins of Amphibious Fishes

Author

Lorente-Martínez, Héctor, Agorreta, Ainhoa, Irisarri, Iker, Zardoya, Rafael, Edwards, Scott V., and San Mauro, Diego

Abstract

Aquaporins (AQPs) are a highly diverse family of transmembrane proteins involved in osmotic regulation that played an important role in the conquest of land by tetrapods. However, little is known about their possible implication in the acquisition of an amphibious lifestyle in actinopterygian fishes. Herein, we investigated the molecular evolution of AQPs in 22 amphibious actinopterygian fishes by assembling a comprehensive dataset that was used to (1) catalogue AQP paralog members and classes; (2) determine the gene family birth and death process; (3) test for positive selection in a phylogenetic framework; and (4) reconstruct structural protein models. We found evidence of adaptive evolution in 21 AQPs belonging to 5 different classes. Almost half of the tree branches and protein sites that were under positive selection were found in the AQP11 class. The detected sequence changes indicate modifications in molecular function and/or structure, which could be related to adaptation to an amphibious lifestyle. AQP11 orthologues appear to be the most promising candidates to have facilitated the processes of the water-to-land transition in amphibious fishes. Additionally, the signature of positive selection found in the AQP11b stem branch of the Gobiidae clade suggests a possible case of exaptation in this clade.

Published
2023

30. Automatic Prediction of the Genetic Code

Author

Patricio, Mateus, Huerta-Cepas, Jaime, Gabaldón, Toni, Zardoya, Rafael, Posada, David, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Omatu, Sigeru, editor, Rocha, Miguel P., editor, Bravo, José, editor, Fernández, Florentino, editor, Corchado, Emilio, editor, Bustillo, Andrés, editor, and Corchado, Juan M., editor

Published
2009
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32. Microsatellite records for volume 8, issue 1

Author

Arias, Maria Cristina, Aulagnier, Stéphane, Baerwald, Erin F., Barclay, Robert M. R., Batista, Jacqueline Silva, Beasley, Rochelle R., Bezerra, Rodrigo A., Blanc, Frédéric, Bridge, Eli S., Cabria, Maria Teresa, Caputo, Lívia Izabela, Chen, Jie, Chen, Jian-Hua, Chen, Zhi, Chen, Ching-Hung, Chu, Pengfei, Contina, Andrea, da Silva Carmo, Fausto Moreira, de Carvalho, Leiliane Campos, de Freitas Viana, Priscila Maria, de Macêdo, Jeferson Luis Vasconcelos, de Menezes Yazbeck, Gabriel, de Oliveira Teixeira, Zélia, de Souza Araujo, Natália, Dequigiovanni, Gabriel, Ding, Shaoxiong, Dos Santos, Priscila Karla Ferreira, Ernest, Holly B., Feng, Yan-Wei, Formiga, Kyara Martins, Fournier-Chambrillon, Christine, Françoso, Elaine, Fu, Yaru, Gagne, Roderick B., Gaiotto, Fernanda A., Gao, Tian-xiang, Ge, Hongzi, Ge, Taiming, Gillet, François, Gong, Yun, Gong, Hong-mei, Guo, Qiqiang, Guo, Liang, Guo, Liang, Harrigan, Ryan J., He, Libo, House, Carrie J., Der Hsiao, Chung-, Huang, Rong, Iyengar, Arati, Jiang, Xiayun, Jiang, Hai-Lin, Johnson, Tania A., Jones, Kenneth L., Kageyama, Paulo Yoshio, Kelly, Jeffrey F., Lam, Lydia, Lance, Stacey L., Li, Hong, Li, Cheng, Li, Fugui, Li, Huie, Li, Shaoke, Li, Yongming, Li, Mingming, Li, Mingming, Li, Fuhua, Li, Wei-guo, Li, Jitao, Li, Jian, Li, Xinru, Liang, Kai, Liang, Yaosi, Liao, Fuchu, Liao, Lanjie, Lin, Haoran, Lin, Haoran, Lin, Haoran, Lin, Qiang, Liu, Hong, Liu, Honggao, Liu, Lu, Liu, Xiang-Quan, Liu, Ping, Liu, Chen, Liu, Xin, Lopes, Maria Teresa Gomes, Lu, Danqi, Luan, Ming-Bao, Luo, Wei, Meng, Zining, Meng, Zining, Michaux, Johan R., Némoz, Mélanie, Pollinger, John P., Qiao, Ye, Qu, Hongyue, Ramos, Santiago Linorio Ferreyra, Le Roux, Stephné, Santiago, Leandro Rodrigues, Shao, Xiaoyan, Shen, Kang-Ning, Shen, Heding, Shen, Hao, Smith, Thomas B., Song, Dang-yu, Sourp, Eric, Sun, Yiwen, Tang, Huiyuan, Tang, Qing, Tong, Yiqin, van den Einden, Marion, van Hoppe, Moniek J. C., Veasey, Elizabeth Ann, Vial-Novella, Corinne, Wan, Li, Wang, Xiaojun, Wang, Yiming, Wang, Yu, Wang, Yaping, Wang, Ruoran, Wang, Xin, Wang, Rifang, Wang, Quanchao, Wang, Guo-dong, Wang, Jiajia, Wang, Dongfeng, Wang, Peipei, Wei, Xiu-Mei, Wen, Yanfei, Wen, Haishen, Wu, Xue-Ping, Wu, Xin, Xiang, Jianhai, Xie, Zhenzhen, Xu, Zhanning, Xu, Pao, Yang, Zhi, Yang, Sen, Yang, Sen, Yin, Cece, Yin, Shaowu, Yin, Shaowu, Yu, Yang, Yuan, Xiping, Yue, Gen Hua, Zang, Gong-Gu, Zardoya, Rafael, Zhang, Li-hui, Zhang, Xiaojun, Zhang, Yong, Zhang, Guosong, di Zhang, Yan-, Zhang, Hongye, Zhang, Guosong, Zhao, Jie, Zhao, Cheng, Zhu, Fei, Zhu, Hongchai, Zhu, Shilong, and Zou, Shuming

Published
2016
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37. Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics.

Author

Herráez-Pérez, Ana, Pardos-Blas, José Ramón, Afonso, Carlos M L, Tenorio, Manuel J, and Zardoya, Rafael

Subjects
CONUS, GENOME size, NEOGASTROPODA, CHROMOSOMES, DRUG development
Abstract

Background Genomes are powerful resources to understand the evolutionary mechanisms underpinning the origin and diversification of the venoms of cone snails (Conidae: Caenogastropoda) and could aid in the development of novel drugs. Findings Here, we used PacBio continuous long reads and Omni-C data to assemble the chromosome-level genome of Kalloconus canariensis , a vermivorous cone endemic to the Canary Islands. The final genome size was 2.87 Gb, with a N50 of 79.75 Mb and 91% of the reads located into the 35 largest scaffolds. Up to 55.80% of the genome was annotated as repetitive regions, being class I of transposable elements (16.65%) predominant. The annotation estimated 34,287 gene models. Comparative analysis of this genome with the 2 cone snail genomes released to date (Dendroconus betulinus and Lautoconus ventricosus) revealed similar genome sizes and organization, although chromosome sizes tended to be shorter in K. canariensis. Phylogenetic relationships within subclass Caenogastropoda were recovered with strong statistical support. The family Conidae was recovered as a clade, with K. canariensis plus L. ventricosus sister to D. betulinus. Conclusions Despite the great diversity of cone snails (>900 species) and their venoms (hundreds of peptides per species), only 2 recently reported genomes are available for the group. The high-quality chromosome-level assembly of K. canariensis will be a valuable reference for studying the origin and evolution of conotoxin genes as well as whole-genome duplication events during gastropod evolution. [ABSTRACT FROM AUTHOR]

Published
2023
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41. EVOLUTIONARY BIOLOGY IN BIODIVERSITY SCIENCE, CONSERVATION, AND POLICY: A CALL TO ACTION

Author

Hendry, Andrew P., Lohmann, Lúcia G., Conti, Elena, Cracraft, Joel, Crandall, Keith A., Faith, Daniel P., Häuser, Christoph, Joly, Carlos A., Kogure, Kazuhiro, Larigauderie, Anne, Magallón, Susana, Moritz, Craig, Tillier, Simon, Zardoya, Rafael, Prieur-Richard, Anne-Hélène, Walther, Bruno A., Yahara, Tetsukazu, and Donoghue, Michael J.

Published
2010

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