Anderson, United States
Anderson, United States

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Abernathy J.,Aquatic Genomics Unit | Xu D.-H.,Aquatic Animal Health Research Unit | Peatman E.,Aquatic Genomics Unit | Kucuktas H.,Aquatic Genomics Unit | And 2 more authors.
Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics | Year: 2011

The ciliate parasite Ichthyophthirius multifiliis (Ich) infects many freshwater fish, causing white spot disease that leads to heavy economic losses to aquaculture and ornamental industries. Despite its economic importance, molecular studies examining fundamental processes such as life stage regulation and infectivity have been scarce. In this study, we developed an oligo microarray platform using all available I. multifiliis expressed sequence tag (EST) information as well as probes designed through comparative genomics to other protozoa. Gene expression profiling for developmental and virulence factors was conducted using this platform. For the developmental study, the microarray was used to examine gene expression profiles between the three major life stages of Ich: infective theront, parasitic trophont, and reproductive tomont. A total of 135 putative I. multifiliis genes were found to be differentially expressed among all three life-stages. Examples of differentially expressed transcripts among life stages include immobilization antigens and epiplasmin, as well as various other transcripts involved in developmental regulation and host-parasite interactions. I. multifiliis has been shown to lose infectivity at later cell divisions potentially due to cellular senescence. Therefore, the microarray was also used to explore expression of senescence-associated genes as related to the passage number of the parasite. In this regard, comparison between tomont early and late passages yielded 493 differently expressed genes; 1478 differentially expressed genes were identified between trophont early and late passages. The EST-derived oligo microarray represents a first generation array of this ciliate and provided reproducible expression data as validated by quantitative RT-PCR. © 2011 Elsevier Inc.


Zeng Q.,Aquatic Genomics Unit | Liu S.,Aquatic Genomics Unit | Yao J.,Aquatic Genomics Unit | Zhang Y.,Aquatic Genomics Unit | And 7 more authors.
Biology of Reproduction | Year: 2016

Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture species in the United States. It is also a suitable model for studying the mechanisms of sex determination and differentiation because of its sexual plasticity and exhibition of both genetic and environmental sex determination. The testicular differentiation in male channel catfish normally starts between 90 and 102 days postfertilization (dpf), while the ovarian differentiation starts early from 19 dpf. As such, efforts to better understand the postponed testicular development at the molecular level are needed. Toward that end, we conducted transcriptomic comparison of gene expression of male and female gonads at 90, 100, and 110 dpf using high-throughput RNA-Seq. Transcriptomic profiles of male gonads on 90 and 100 dpf exhibited high similarities except for a small number of significantly up-regulated genes that were involved in development of germ cell-supporting somatic cells, while drastic changes were observed during 100-110 dpf, with a group of highly up-regulated genes that were involved in germ cells development, including nanog and pou5f1. Transcriptomic comparison between testes and ovaries identified male-preferential genes, such as gsdf, cxcl12, as well as other cytokines mediated the development of the gonad into a testis. Coexpression analysis revealed highly correlated genes and potential pathways underlying germ cell differentiation and spermatogonia stem cell development. The candidate genes and pathways identified in this study set the foundation for further studies on sex determination and differentiation in catfish as well as other teleosts. © 2016 by the Society for the Study of Reproduction, Inc.


Lu J.,Aquatic Genomics Unit | Peatman E.,Aquatic Genomics Unit | Yang Q.,Auburn University | Wang S.,Aquatic Genomics Unit | And 4 more authors.
Nucleic Acids Research | Year: 2011

The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome. org. © The Author(s) 2010.


PubMed | Aquatic Genomics Unit
Type: Journal Article | Journal: Biology of reproduction | Year: 2016

Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture species in the United States. It is also a suitable model for studying the mechanisms of sex determination and differentiation because of its sexual plasticity and exhibition of both genetic and environmental sex determination. The testicular differentiation in male channel catfish normally starts between 90 and 102 days postfertilization (dpf), while the ovarian differentiation starts early from 19 dpf. As such, efforts to better understand the postponed testicular development at the molecular level are needed. Toward that end, we conducted transcriptomic comparison of gene expression of male and female gonads at 90, 100, and 110 dpf using high-throughput RNA-Seq. Transcriptomic profiles of male gonads on 90 and 100 dpf exhibited high similarities except for a small number of significantly up-regulated genes that were involved in development of germ cell-supporting somatic cells, while drastic changes were observed during 100-110 dpf, with a group of highly up-regulated genes that were involved in germ cells development, including nanog and pou5f1 Transcriptomic comparison between testes and ovaries identified male-preferential genes, such as gsdf, cxcl12, as well as other cytokines mediated the development of the gonad into a testis. Co-expression analysis revealed highly correlated genes and potential pathways underlying germ cell differentiation and spermatogonia stem cell development. The candidate genes and pathways identified in this study set the foundation for further studies on sex determination and differentiation in catfish as well as other teleosts.

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