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6. Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) Coinfection Downregulate Immune-Relevant Pathways and Cause Splenic and Kidney Necrosis in Barramundi Under Commercial Farming Conditions

Author

Domingos, Jose A., primary, Shen, Xueyan, additional, Terence, Celestine, additional, Senapin, Saengchan, additional, Dong, Ha Thanh, additional, Tan, Marie R., additional, Gibson-Kueh, Susan, additional, and Jerry, Dean R., additional

Published
2021
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8. Fox gene loci in Takifugu rubripes and Tetraodon nigroviridis genomes and comparison with those of medaka and zebrafish genomes

Author

Shen, Xueyan, Cui, Jianzhou, and Gong, Qingli

Subjects
Genomes -- Physiological aspects -- Comparative analysis, Zebra fish -- Physiological aspects -- Genetic aspects, Transcription factors -- Physiological aspects, Biological sciences
Abstract

Members of the Fox gene family of transcriptional regulators are essential for animal development and have been extensively studied in vertebrates. The mouse and human genomes contain at least 40 FOX genes which are divided into 19 subclasses based on the sequence similarity of the highly conserved forkhead domain. Using the genome sequence of the Takifugu rubripes and Tetraodon nigroviridis, we examined the genomic complement of fox genes in these organisms to gain insight into the evolutionary relationship of this gene family. We identified 53 fox genes in Tetraodon nigroviridis and Takifugu rubripes genome by searching the forkhead domain. These genes are divided into 18 subclasses as follows: 8 fox genes in subclass O; 6 in subclass P ; 4 in subclasses D, J, and N; 3 in subclasses A, B, C, E, F, and I; 2 in subclasses K, L, and Q; and 1 in subclasses G, H, M, and R. Together with the forkhead domain sequences of human, chicken, frog, zebrafish, medaka, and Caenorhabditis elegans, the phylogenetic relationship of the fox genes in Takifugu rubripes and Tetraodon nigroviridis were analyzed and compared. The genes structure, general features, and the three-dimensional model of these genes were also discussed. Key words: Tetraodon nigroviridis, Takifugu rubripes, Forkhead, genome duplication, evolution. Les membres de la famille des genes Fox de regulateurs transcriptionnels sont essentiels au developpement chez les animaux et ils ont ete etudies en detail chez les vertebres. Les genomes humain et murin comptent plus de 40 genes FOX qui sont divises en 19 sous-classes sur la base de la similarite des sequences au sein de la region conservee que constitue le domaine forkhead. A l'aide de la sequence genomique du Takifugu rubripes et du Tetraodon nigroviridis, les auteurs ont examine le complement de genes fox chez ces especes pour en apprendre davantage sur les relations evolutives au sein de cette famille de genes. Les auteurs ont identifie 53 genes fox au sein des genomes du Tetraodon nigroviridis et du Takifugu rubripes en recherchant le domaine forkhead. Ces genes forment 18 sous-classes de la maniere suivante : 8 genes fox font partie de la sous-classe O; 6 forment la sous-classe P; 4 appartiennent aux sous-classes D, J et N; 3 font partie des sous-classes A, B, C, E, F et I; 2 appartiennent aux sous-classes K, L et Q; et 1 seul forment les sous-classes G, H, M et R. En prenant les sequences des domaines forkhead des genes de l' humain, du poulet, de la grenouille, du poisson zebre, du medaka et du Caenorhabditis elegans, les relations phylogenetiques des genes fox du Takifugu rubripes et du Tetraodon nigroviridis ont ete analysees et comparees. La structure des genes, leurs proprietes generales et les modeles tridimensionnels de ces genes sont egalement discutes. Mots-cles : Tetraodon nigriviridis, Takifugu rubripes, Forkhead, duplication genomique, evolution. [Traduit par la Redaction], Introduction The FOX genes are members of the forkhead/winged helix family of transcription factors. These genes play important roles in a variety of developmental processes, including germ layer specification, gastrulation, [...]

Published
2011
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10. An Enriched Environment Enhances Angiogenesis Surrounding the Cingulum in Ischaemic Stroke Rats

Author

Shen, Xueyan, primary, Luo, Lu, additional, Wang, Fei, additional, Yu, Kewei, additional, Xie, Hongyu, additional, Tian, Shan, additional, Liu, Gang, additional, Bao, Chunrong, additional, Fan, Yunhui, additional, Xing, Ying, additional, Wang, Nianhong, additional, Li, Siyue, additional, Liu, Li, additional, Zhang, Qun, additional, and Wu, Yi, additional

Published
2020
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12. Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

Author

Vij, Shubha, primary, Kuhl, Heiner, additional, Kuznetsova, Inna S., additional, Komissarov, Aleksey, additional, Yurchenko, Andrey A., additional, Van Heusden, Peter, additional, Singh, Siddharth, additional, Thevasagayam, Natascha M., additional, Prakki, Sai Rama Sridatta, additional, Purushothaman, Kathiresan, additional, Saju, Jolly M., additional, Jiang, Junhui, additional, Mbandi, Stanley Kimbung, additional, Jonas, Mario, additional, Hin Yan Tong, Amy, additional, Mwangi, Sarah, additional, Lau, Doreen, additional, Ngoh, Si Yan, additional, Liew, Woei Chang, additional, Shen, Xueyan, additional, Hon, Lawrence S., additional, Drake, James P., additional, Boitano, Matthew, additional, Hall, Richard, additional, Chin, Chen-Shan, additional, Lachumanan, Ramkumar, additional, Korlach, Jonas, additional, Trifonov, Vladimir, additional, Kabilov, Marsel, additional, Tupikin, Alexey, additional, Green, Darrell, additional, Moxon, Simon, additional, Garvin, Tyler, additional, Sedlazeck, Fritz J., additional, Vurture, Gregory W., additional, Gopalapillai, Gopikrishna, additional, Katneni, Vinaya Kumar, additional, Noble, Tansyn H., additional, Scaria, Vinod, additional, Sivasubbu, Sridhar, additional, Jerry, Dean R., additional, O'Brien, Stephen J., additional, Schatz, Michael C., additional, Dalmay, Tamás, additional, Turner, Stephen W., additional, Lok, Si, additional, Christoffels, Alan, additional, and Orbán, László, additional

Published
2016
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13. A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

Author

Li, Jia, primary, Bian, Chao, additional, Hu, Yinchang, additional, Mu, Xidong, additional, Shen, Xueyan, additional, Ravi, Vydianathan, additional, Kuznetsova, Inna S., additional, Sun, Ying, additional, You, Xinxin, additional, Qiu, Ying, additional, Zhang, Xinhui, additional, Yu, Hui, additional, Huang, Yu, additional, Xu, Pao, additional, Gu, Ruobo, additional, Xu, Junmin, additional, Orbán, László, additional, Venkatesh, Byrappa, additional, and Shi, Qiong, additional

Published
2016
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14. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

Author

Bian, Chao, primary, Hu, Yinchang, additional, Ravi, Vydianathan, additional, Kuznetsova, Inna S., additional, Shen, Xueyan, additional, Mu, Xidong, additional, Sun, Ying, additional, You, Xinxin, additional, Li, Jia, additional, Li, Xiaofeng, additional, Qiu, Ying, additional, Tay, Boon-Hui, additional, Thevasagayam, Natascha May, additional, Komissarov, Aleksey S., additional, Trifonov, Vladimir, additional, Kabilov, Marsel, additional, Tupikin, Alexey, additional, Luo, Jianren, additional, Liu, Yi, additional, Song, Hongmei, additional, Liu, Chao, additional, Wang, Xuejie, additional, Gu, Dangen, additional, Yang, Yexin, additional, Li, Wujiao, additional, Polgar, Gianluca, additional, Fan, Guangyi, additional, Zeng, Peng, additional, Zhang, He, additional, Xiong, Zijun, additional, Tang, Zhujing, additional, Peng, Chao, additional, Ruan, Zhiqiang, additional, Yu, Hui, additional, Chen, Jieming, additional, Fan, Mingjun, additional, Huang, Yu, additional, Wang, Min, additional, Zhao, Xiaomeng, additional, Hu, Guojun, additional, Yang, Huanming, additional, Wang, Jian, additional, Wang, Jun, additional, Xu, Xun, additional, Song, Linsheng, additional, Xu, Gangchun, additional, Xu, Pao, additional, Xu, Junmin, additional, O’Brien, Stephen J., additional, Orbán, László, additional, Venkatesh, Byrappa, additional, and Shi, Qiong, additional

Published
2016
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15. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

Author

Vij, Shubha, primary, Kuhl, Heiner, additional, Kuznetsova, Inna S., additional, Komissarov, Aleksey, additional, Yurchenko, Andrey A., additional, Van Heusden, Peter, additional, Singh, Siddharth, additional, Thevasagayam, Natascha M., additional, Prakki, Sai Rama Sridatta, additional, Purushothaman, Kathiresan, additional, Saju, Jolly M., additional, Jiang, Junhui, additional, Mbandi, Stanley Kimbung, additional, Jonas, Mario, additional, Hin Yan Tong, Amy, additional, Mwangi, Sarah, additional, Lau, Doreen, additional, Ngoh, Si Yan, additional, Liew, Woei Chang, additional, Shen, Xueyan, additional, Hon, Lawrence S., additional, Drake, James P., additional, Boitano, Matthew, additional, Hall, Richard, additional, Chin, Chen-Shan, additional, Lachumanan, Ramkumar, additional, Korlach, Jonas, additional, Trifonov, Vladimir, additional, Kabilov, Marsel, additional, Tupikin, Alexey, additional, Green, Darrell, additional, Moxon, Simon, additional, Garvin, Tyler, additional, Sedlazeck, Fritz J., additional, Vurture, Gregory W., additional, Gopalapillai, Gopikrishna, additional, Kumar Katneni, Vinaya, additional, Noble, Tansyn H., additional, Scaria, Vinod, additional, Sivasubbu, Sridhar, additional, Jerry, Dean R., additional, O'Brien, Stephen J., additional, Schatz, Michael C., additional, Dalmay, Tamás, additional, Turner, Stephen W., additional, Lok, Si, additional, Christoffels, Alan, additional, and Orbán, László, additional

Published
2016
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16. Nutrigenomic and Nutritional Analyses Reveal the Effects of Pelleted Feeds on Asian Seabass (Lates calcarifer)

Author

Ngoh, Si Yan, primary, Tan, Daniel, additional, Shen, Xueyan, additional, Kathiresan, Purushothaman, additional, Jiang, Junhui, additional, Liew, Woei Chang, additional, Thevasagayam, Natascha May, additional, Kwan, Hsiao Yuen, additional, Saju, Jolly M., additional, Prakki, Sridatta R. S., additional, Goh, Chin Heng, additional, Wong, Hong Ching, additional, Chan, Tai Teck, additional, Mézes, Miklós, additional, and Orbán, László, additional

Published
2015
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18. Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer)

Author

Thevasagayam, Natascha, primary, Sridatta, Prakki, additional, Jiang, Junhui, additional, Tong, Amy, additional, Saju, Jolly, additional, Kathiresan, Purushothaman, additional, Kwan, Hsiao, additional, Ngoh, Si, additional, Liew, Woei, additional, Kuznetsova, Inna, additional, Shen, Xueyan, additional, Lok, Si, additional, Vij, Shubha, additional, and Orbán, László, additional

Published
2015
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20. Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers.

Author

Shen X, Hu J, Yáñez JM, Bastos Gomes G, Poon ZWJ, Foster D, Alarcon JF, Shao L, Guo X, Shao Y, Huerlimann R, Li C, Goulden E, Anderson K, Fan G, and Domingos JA

Subjects
Male, Animals, Female, Perciformes genetics, Sex Determination Processes genetics, Sex Chromosomes genetics, Genetic Markers, Genome-Wide Association Study, Synteny, Genomics methods, Genome
Abstract

Background: Cobia (Rachycentron canadum) is the only member of the Rachycentridae family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia are completely unknown., Results: Here, we reported 2 high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.51 Mb (contig/scaffold N50: 86.0 kb/24.3 Mb) and 583.88 Mb (79.9 kb/22.5 Mb), respectively. Synteny inference among perciform genomes revealed that cobia and the remora Echeneis naucrates were sister groups. Further, whole-genome resequencing of 31 males and 60 females, genome-wide association study, and sequencing depth analysis identified 3 short male-specific regions within a 10.7-kb continuous genomic region on male chromosome 18, which hinted at an undifferentiated sex chromosome system with a putative XX/XY mode of sex determination in cobia. Importantly, the only 2 genes within/between the male-specific regions, epoxide hydrolase 1 (ephx1, renamed cephx1y) and transcription factor 24 (tcf24, renamed ctcf24y), showed testis-specific/biased gene expression, whereas their counterparts cephx1x and ctf24x, located in female chromosome 18, were similarly expressed in both sexes. In addition, male-specific PCR targeting the cephx1y gene revealed that this genomic feature is conserved in cobia populations from Panama, Brazil, Australia, and Japan., Conclusion: The first comprehensive genomic survey presented here is a valuable resource for future studies on cobia population structure and dynamics, conservation, and evolutionary history. Furthermore, it establishes evidence of putative male heterogametic regions with 2 genes playing a potential role in the sex determination of the species, and it provides further support for the rapid evolution of sex-determining mechanisms in teleost fish., (© The Author(s) 2024. Published by Oxford University Press GigaScience.)

Published
2024
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