Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

Abstract Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we perform...

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Autores principales:	Wu Gan, Yu-Wen Chung-Davidson, Zelin Chen, Shiying Song, Wenyao Cui, Wei He, Qinghua Zhang, Weiming Li, Mingyou Li, Jianfeng Ren
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/00a22ac057874f8dba1be05dc18bdcb8
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spelling	oai:doaj.org-article:00a22ac057874f8dba1be05dc18bdcb82021-12-02T10:49:34ZGlobal tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish10.1038/s41598-020-80168-62045-2322https://doaj.org/article/00a22ac057874f8dba1be05dc18bdcb82021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80168-6https://doaj.org/toc/2045-2322Abstract Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we performed a large-scale transcriptomic sequencing on 13 adult goldfish tissues, larvae at one- and three-days post hatch, and skin tissues with four different color pigmentation. A total of 25.52 Gb and 149.80 Gb clean data were obtained using the PacBio and Illumina platforms, respectively. Onto the goldfish reference genome, we mapped 137,674 non-redundant transcripts, of which 5.54% was known isoforms and 78.53% was novel isoforms of the reference genes, and the remaining 21,926 isoforms are novel isoforms of additional new genes. Both skin-specific and color-specific transcriptomic analyses showed that several significantly enriched genes were known to be involved in melanogenesis, tyrosine metabolism, PPAR signaling pathway, folate biosynthesis metabolism and so on. Thirteen differentially expressed genes across different color skins were associated with melanogenesis and pteridine synthesis including mitf, ednrb, mc1r, tyr, mlph and gch1, and xanthophore differentiation such as pax7, slc2a11 and slc2a15. These transcriptomic data revealed pathways involved in goldfish pigmentation and improved the gene annotation of the reference genome.Wu GanYu-Wen Chung-DavidsonZelin ChenShiying SongWenyao CuiWei HeQinghua ZhangWeiming LiMingyou LiJianfeng RenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wu Gan Yu-Wen Chung-Davidson Zelin Chen Shiying Song Wenyao Cui Wei He Qinghua Zhang Weiming Li Mingyou Li Jianfeng Ren Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
description	Abstract Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we performed a large-scale transcriptomic sequencing on 13 adult goldfish tissues, larvae at one- and three-days post hatch, and skin tissues with four different color pigmentation. A total of 25.52 Gb and 149.80 Gb clean data were obtained using the PacBio and Illumina platforms, respectively. Onto the goldfish reference genome, we mapped 137,674 non-redundant transcripts, of which 5.54% was known isoforms and 78.53% was novel isoforms of the reference genes, and the remaining 21,926 isoforms are novel isoforms of additional new genes. Both skin-specific and color-specific transcriptomic analyses showed that several significantly enriched genes were known to be involved in melanogenesis, tyrosine metabolism, PPAR signaling pathway, folate biosynthesis metabolism and so on. Thirteen differentially expressed genes across different color skins were associated with melanogenesis and pteridine synthesis including mitf, ednrb, mc1r, tyr, mlph and gch1, and xanthophore differentiation such as pax7, slc2a11 and slc2a15. These transcriptomic data revealed pathways involved in goldfish pigmentation and improved the gene annotation of the reference genome.
format	article
author	Wu Gan Yu-Wen Chung-Davidson Zelin Chen Shiying Song Wenyao Cui Wei He Qinghua Zhang Weiming Li Mingyou Li Jianfeng Ren
author_facet	Wu Gan Yu-Wen Chung-Davidson Zelin Chen Shiying Song Wenyao Cui Wei He Qinghua Zhang Weiming Li Mingyou Li Jianfeng Ren
author_sort	Wu Gan
title	Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
title_short	Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
title_full	Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
title_fullStr	Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
title_full_unstemmed	Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
title_sort	global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/00a22ac057874f8dba1be05dc18bdcb8
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Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

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