| Cyprinidae almost distribute all over the world which is native to North America, Africa and Eurasia. The richness of cyprinidae species in all continents are seriously imbalance due to many reasons. Asian contains almost all the sub-groups including the most abundant species diversity, whereas Europe is the scarcest. China, which is located in East Asia, is one of the world’s largest cyprinidae species countries. Cyprinid is a freshwater fish which mainly distributed in the freshwater environment, but some species are able to survive and breed in saline water environment. As an important economic aquatic species, C. carpio(common carp) and L. waleckii(Amur ide) have been widespread concerned and researched. Dispite their economic value, common carp and Amur ide has a very important biological significance for the study of scientific problems and provide good biological materials. For example: common carp as an allotetraploid organism provides an important model for the study of gene duplication, chromosomes and genome doubling; moreover, Amur ide provides important material for the study of phylogeny and biological mechanisms under high salinity stress environment, because of its strong salinity resistance. In view of their significance economic and research value, we carried out a series of studies of these species, including the following three aspects: 1. Phylogeny and Evolution of Multiple Common Carp Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial GenomesCommon carp is one of the oldest, most widely farmed commercially important freshwater fish in the world. Common carp have a cultural history and domestication of several thousand years and have become one of the most important edible and popular aquarium fish, comprising a large number of strains worldwide. In spit of these differences offer rich germplasm resources for the work of genetic selection, the phenomenon of multiple hybridization and genetic infiltration often makes the genetic background more complex and vague between different subspecies and strains as well as the phylogenetic relationship. These exist problems need a more integrated application genetic tools and more extensive research objectives to solve.Herein, we utilized the high-throughput whole-genome resequencing data of 26 common carp individuals from nine strains and extracted the complete mitochondrial genome sequences(CMG) using a bioinformatics approach. The CMG were collected, assembled, and subjected to a phylogenetic analysis of these individuals as well as Cyt b and D-loop. Utilizing CMG sequences will provide additional resolution to decipher difficult phylogenetic relationships and benefit germplasm conservation and genetic breeding efforts for common carp. The resolved and stated issues are as follows:1.1 The European and Asian common carp strains should belong to different subspecies because of their distantly genetic relationship;1.2 Our data suggest that Xingguo carp(XC) is more closely related to Hebao carp than Oujiang carp, which is consistent with the biogeographic evidence;1.3 We suggest that ancestral populations of Koi or Thailand carp may have originated from Oujiang carp, or they could have the same origin;1.4 Songpu carp(SP) is a Chinese domesticated mirror carp strain based on German mirror carp and was introduced to China in the 1970 s. Breeding records showthat no hybrids with Asian strains have occurred. Thus, SP genetically belongs to the European subspecies. A phylogenetic study based on genome-wide SNP loci confirmed consanguinity. Surprisingly, our results show that SP was closely clustered with XC based on the very small genetic distance. The only reasonable explanation is that XC was the maternal parent when SP was domesticated in the 1970 s. Therefore, we suggest that European mirror carp was first hybridized with XC to enhance adaptability after its introduction into China and was then backcrossed continuously with European mirror carp to achieve desired traits, such as high growth rate and stress tolerance. SP was selected with stable traits and performance after several rounds of backcrossing and introgression;1.5 We clearly stated that in common carp D-loop can replace the CMG in the analysis of phylogenetic. In aquaculture, we firstly applicated the bioinformation methods to analyse the mitochondrial genome data retrievaled from the genome data, which found another way for for the future analysis. 2. The Phylogenetic Relationship between L.waleckii Inhabiting in Alkaline Water and FreshwaterAmur ide belongs to the family of cyprinid, distributing in the Amur River basin in Russia, Mongolia, China and Korea as well as some inland lakes(Dali Nor Lake) in Inner Mongolia around China. Although Amur ide inhabits in fresh water, it also has great tolerance on high salinity and alkalinity environment. For example, Amur ide inhabiting in Dali Nor lake, one of the most renowned typical saline-alkaline lake with high concentrations of carbonate salts. Moreover, from the espect of ecology, Amur ide which is also ecologically important fish to migrating birds that stop over at Dali Nor Lake and feed on them during their journeys from Siberia to the south. Because of its high tolerance to increased salinity and alkalinity, Amur ide has been recently developed as a potential aquaculture species in the severe environment. In spite of economic and ecological importance, the mechanism of its tolerance on high alkalinity and salinity is still unclear. Rarely genetic resources have been minimally developed due to few physiological and genetic studies have been performed. To date, there are only a few analysis showed some differences in alkaline and salinity tolerance and population difference between the Dali Nor Lake and the freshwater populations. The main contents and conclusions are as follows:2.1 Firstly, we determined the whole mitogenome sequences for 30 individuals of 2 populations from the Dali Basin and the Amur Basin, which occupying adjacent, but contrasting, environments(alkaline water vs. freshwater);2.2 Secondly, we analyze the basic information of mitochondrial genome; then apply the genetic information of mitochondrial genome to analyze the haplotype, phylogenetic, differentiation time, and nucleotide polymorphism;2.3 The results showed that in the freshwater environment the Amur ide subject to less pressure, the mitochondrial genome has a rapid variation rate, population has a rapid evolution and a wide range of differentiation time, otheirwise the Amur ide which living in saline water environment has the opposite conclusions;2.4 This study provides an important reference for the research of aquatic resistance as well as evolution and differentiation of group in inverse environment. 3. Phylogenetic and Evolutionary Analyses of the Frizzled Gene Family in Common CarpIn humans, the Frizzled(FZD) gene family encodes 10 homologous proteins that commonly localize to the plasma membrane. Besides being associated with three main signaling pathways for cell development, most FZDs have different physiological effects and are major determinants in the development process of vertebrates. Here, we identified and annotated the FZD genes in the whole-genome and multiple transcriptome database of common carp(Cyprinus carpio), a teleost fish, and determined their phylogenetic relationships to FZDs in other vertebrates. Then we analyzed the synteny of FZD gene family. At last, we performed a RT-PCR analysis using gene-specific primers to check their expression levels in seven adult common carp tissues(brain, heart, spleen, liver, kidney, skin, and blood) and at different development stages post-fertilization(0 hours, 12 hours, 24 hours, 36 hours, 48 hours, 3 days, 5 days, and 7 days). We mainly carried out the analysis of phylogeny, evolution and expression in FZD gene family, verified the result of genome, and discussed the gene fate after the fourth round of genome replication in common carp. Our study has provided insights into gene duplication, divergence post multiple rounds of whole genome duplications, and gene expression profiles in different tissues and stages in common carp. The main contents and conclusions are as follows:3.1 Our analyses revealed extensive gene duplications in the common carp that have led to the 26 FZD genes that we detected in the common carp genome.3.2 All 26 FZD genes were assigned orthology to the 10 FZD genes of on-land vertebrates, with none of genes being specific to the fish lineage.3.3 We postulated that the expansion of the FZD gene family in common carp was the result of an additional whole genome duplication event and that the FZD gene family in other teleosts has been lost in their evolution history with the reason that the functions of genes are redundant and conservation.3.4 Under selection pressure, gene loss may have occurred quickly after the WGD events so as to maintain the single copy of FZD6. The FZD6 protein sequences were found to be highly conserved across all the vertebrate species, suggesting that the conserved FZD6 gene is critical for survivability and very little change is allowed in its coding sequence and copy number.3.5 Through the expression profiling of FZD genes in common carp, we speculate that the ancestral gene was likely capable of performing all functions and was expressed broadly, while some descendant duplicate genes only performed partial functions and were specifically expressed at certain stages of development. |
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