Exploration of Molecular Mechanism of Skin Albinism in Albino Northern Snakehead Channa argus var.(Teleostei: Channidae) Based on Transcriptome Sequencing
LI Yan1, ZHOU Yan1, LEI Luo2, SU Jian3, FAN Wei3, LUO Yu3, LI Junting1, GAO He1, ZHOU Chaowei1
1. College of Fisheries, Southwest University, Chongqing 402460, China; 2. Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; 3. Neijiang City Academy of Agricultural Sciences, Neijiang 641000, China
Abstract：In order to understand the molecular regulatory mechanism in albino northern snakehead Channa argus, Illumina Hiseq technology was used to define the transcriptome of albino northern snakehead C. argus var., a color variety of northern snakehead skin. DEseq analysis revealed that 694 genes were found to be significantly differentially expressed.Gene ontology analysis indicated that many of these genes encoded proteins involved in cellular process, metabolic process, cell junction and transporter activity. Based on KEGG pathway analysis, DEGs were significantly enriched in tyrosine metabolism pathway, which was involved in skin albinism. The SNP and INDEL analysis showed that there was the more homozygous SNP and INDEL sites in albino northern snakehead than that in northern snakehead, but fewer number of heterozygous SNP and INDEL sites. Furthermore, the predicted genes in the tyrosine metabolic pathway, in which there were SNP non-synonymous coding in hgd and adh5 genes, but no SNPS and INDEL mutation sites were found in tyrp1 gene. Therefore, these results suggest that the skin albinism of northern snakehead be related to tyrosine metabolic pathway, and the decrease in melanin-related genes expression which reduces the skin pigments deposition. The finding will also provide a foundation for further understanding of the molecular mechanism of albino northern snakehead.
[1]于道德,张少春,宋静静,等.鱼类色素细胞及其生态学意义概述[J].广西科学院学报,2020,36(2):117-123. [2]黄冰,郭华荣,张士璀.鱼类白化病的研究进展[J].海洋科学,2003,27(5):11-14. [3]ZHANG S Y, LI X, PAN J L, et al. Use of comparative transcriptome analysis to identify candidate genes related to albinism in channel catfish (Ictalurus punctatus)[J].Aquaculture,2019,500:75-81. [4]HARPER D C, THEOS A C, HERMAN K E, et al. Premelanosome amyloid-like fibrils are composed of only Golgi-processed forms of Pmel17 that have been proteolytically processed in endosomes[J].Journal of Biological Chemistry,2008,283(4):2307-2322. [5]JIANG Y L, ZHANG S H, XU J, et al. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp[J].PLoS One,2014,9(9):e108200. [6]DALY C M S, GROSS J M. Zebrafish snow white as a model for oculocutaneous albinism disorders[J].Investigative Ophthalmology & Visual Science,2010,51(13):3670. [7]CHAVAN B B, SUNDARAM S, SAWANT A D, et al. Record of complete albinism in marine catfish, Osteogeneiosus militaris (Linnaeus, 1758), landed at Mumbai[J].Marine Fisheries Information Service: Technical and Extension Series,2008(197):15-17. [8]TERRY M I, MALLONA I. First record of albinism in salema, Sarpa salpa (Perciformes:Sparidae), in the Mediterranean Sea[J].Marine Biodiversity Records,2015,8:e93. [9]ZHOU A G, XIE S L, FENG Y Y, et al. Insights into the albinism mechanism for two distinct color morphs of northern snakehead, Channa argus through histological and transcriptome analyses[J].Frontiers in Genetics,2020,11:830. [10]FLOREA L, SONG L, SALZBERG S L. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues[J].F1000Research,2013,2:188. [11]ANDERS S, HUBER W. Differential expression analysis for sequence count data[J].Nature Precedings,2010,11:R106. [12]LI H, HANDSAKER B, WYSOKER A, et al. The sequence alignment/map format and SAMtools[J].Bioinformatics,2009,25(16):2078-2079. [13]MCKENNA A, HANNA M, BANKS E, et al. The genome analysis toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J].Genome Research,2010,20(9):1297-1303. [14]孟超,徐皓,黄超,等.鱼类体色相关功能基因的研究进展[J].湖南文理学院学报(自然科学版),2020,32(3):30-35. [15]刘肖莲,李春艳,白晓慧,等.透明草金鱼的皮肤转录组分析[J].水产科学,2022,41(1):110-115. [16]史东杰,陈晓璇,魏东,等.三色锦鲤皮肤转录组测序与功能分析[J].基因组学与应用生物学,2021,40(1):117-127. [17]YAN X Y, WEI L J, HUANG J, et al. Comparative skin transcriptome between common carp and the variety Jinbian carp (Cyprinus carpio v.Jinbian)[J].Aquaculture Research,2020,51(1):187-196. [18]WANG C H, WACHHOLTZ M, WANG J, et al. Analysis of the skin transcriptome in two Oujiang color varieties of common carp[J].PLoS One,2014,9(3):e90074. [19]王金星,赵小凡,周才武,等.乌鳢和白乌鳢的比较研究[J].海洋湖沼通报,1992(2):51-57. [20]王天柱,吴庆,张宁,等.鱼类黑色素合成及信号通路的研究进展[J].中国生物工程杂志,2020,40(5):84-93. [21]TAKAHASHI M, TAKARA K, TOYOZATO T, et al. A novel bioactive chalcone of Morus australis inhibits tyrosinase activity and melanin biosynthesis in B16 melanoma cells[J].Journal of Oleo Science,2012,61(10):585-592. [22]王若青,王娜,王仁凯,等.牙鲆tyrp1a和tyrp1b的鉴定及tyrp1a与mmu-miR-143-5p_R+2的调控关系[J].渔业科学进展,2018,39(2):49-58. [23]BRAASCH I, SCHARTL M, VOLFF J N. Evolution of pigment synthesis pathways by gene and genome duplication in fish[J].BMC Evolutionary Biology,2007,7:74. [24]黎学友,谢明花,黄承勤,等.湖栖鳍虾虎鱼皮肤和眼睛转录组比较[J].水产学报,2021,45(8):1317-1326. [25]CEINOS R M, GUILLOT R, KELSH R N, et al. Pigment patterns in adult fish result from superimposition of two largely independent pigmentation mechanisms[J].Pigment Cell & Melanoma Research,2015,28(2):196-209. [26]王晓谰,吴深基,黄进强,等.虹鳟酪氨酸酶基因的生物信息学分析及其在不同发育阶段和组织中的表达分析[J].中国畜牧兽医,2021,48(5):1516-1524. [27]LUO M K, LU G Q, YIN H R, et al. Fish pigmentation and coloration:molecular mechanisms and aquaculture perspectives[J].Reviews in Aquaculture,2021,13(4):2395-2412. [28]王磊,刘军.黑色素形成分子机制研究进展[J].新疆大学学报(自然科学版),2019,36(4):468-474. [29]DJURDJEVIČ I, FURMANEK T, MIYAZAWA S, et al. Comparative transcriptome analysis of trout skin pigment cells[J].BMC Genomics,2019,20(1):359. [30]DUESTER G, FARRÉS J, FELDER M R, et al. Recommended nomenclature for the vertebrate alcohol dehydrogenase gene family[J].Biochemical Pharmacology,1999,58(3):389-395. [31]HÖÖG J O, HEDBERG J J, STRÖMBERG P, et al. Mammalian alcohol dehydrogenase-functional and struc-tural implications[J].Journal of Biomedical Science,2001,8(1):71-76. [32]FERNÁNDEZ-CAÑÓN J M, GRANADINO B, DE BERNABÉ D B V, et al. The molecular basis of alkaptonuria[J].Nature Genetics,1996,14(1):19-24. [33]JIN W, WEN H B, DU X W, et al. Transcriptome analysis reveals the potential mechanism of the albino skin development in pufferfish Takifugu obscurus[J].In Vitro Cellular & Developmental Biology.Animal,2015,51(6):572-577. [34]LI Y R, GENG X, BAO L S, et al. A deletion in the Hermansky-Pudlak syndrome 4 (Hps4) gene appears to be responsible for albinism in channel catfish[J].Molecular Genetics and Genomics,2017,292(3):663-670. [35]KRAUSS J, GEIGER-RUDOLPH S, KOCH I, et al. A dominant mutation in tyrp1A leads to melanophore death in zebrafish[J].Pigment Cell & Melanoma Research,2014,27(5):827-830. [36]BEIRL A J, LINBO T H, COBB M J, et al. Oca2 regulation of chromatophore differentiation and number is cell type specific in zebrafish[J].Pigment Cell & Melanoma Research,2014,27(2):178-189. [37]GROSS J B. The complex origin of Astyanax cavefish[J].BMC Evolutionary Biology,2012,12:105. [38]PROTAS M E, HERSEY C, KOCHANEK D, et al. Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism[J].Nature Genetics,2006,38(1):107-111. [39]ZOU M, ZHANG X T, SHI Z C, et al. A comparative transcriptome analysis between wild and albino yellow catfish (Pelteobagrus fulvidraco)[J].PLoS One,2015,10(6):e0131504.
2022, Vol. 41 
