大菱鲆抗病相关MHC II B等位基因筛选与分析
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摘要
目前,由于水产业的高速发展,高密度养殖及环境的恶化使水产鱼类病害频发。培育抗病品种,已成为促进水产业发展的一大重要课题。大菱鲆作为我国重要的养殖鱼类,这一难题也急需解决。MHC II B在先天免疫和后天获得性免疫中起着重要作用,并且已有大量研究证明:MHC II B不同等位基因与机体对病原菌的抗性或易感性有着密切关系。所以,我们研究了大菱鲆MHC II B基因的多态性,以及不同等位基因与大菱鲆抗病性之间的关系。
1.大菱鲆致病菌的鉴定
我们通过16S rDNA序列分析鉴定了大菱鲆致病菌-迟钝爱德华氏菌。该病原菌来自于实验室保存菌株,是在大菱鲆疾病暴发时期,从其腹腔内分离获取的单克隆。利用细菌16S rDNA保守区引物8F和1492R扩增其16S rDNA部分序列,并进行克隆测序。通过测序共获得1505bp的序列,所测三个转化子各不相同。将三条序列到Genbank上比对发现,其与两种细菌相似性最高:Edwardsiella ictaluri和Edwardsiella tarda。通过进化树分析可以发现,我们所得到的序列与Edwardsiella tarda亲缘关系最近,而与Edwardsiella ictaluri相差较远。并且其中一条序列16S rDNA-2与Edwardsiella ictaluri和Edwardsiella tarda序列比对时,其与Edwardsiella tarda有100%的相似度。考虑到细菌16S rDNA多拷贝间的差异以及测序误差在内,因此,可以将大菱鲆病原菌鉴定为迟钝爱德华氏菌(Edwardsiella tarda)。
2.大菱鲆MHC II B多态性及其与大菱鲆抗病力的关系
通过对大菱鲆MHC II B内含子1和外显子2的序列分析,共发现了4种不同的内含子1(A、B、C和D型),其不同是由于一19bp重复单元的重复次数不同所致。内含子1的3`端含有一个富含CT/GT的区,该区域为重组酶RecA的潜在识别位点,表明在其演化史中可能发生过重组事件。
通过对43个抗病个体中的224条序列和42个易感个体中的214条序列进行MHC II B外显子2分析,共发现了59个不同的等位基因,其中包括35个A型、6个B型、13个C型和5个D型。对其中的25个等位基因进行了抗病群体与易感群体的分布统计分析,部分等位基因在两个群体中都有分布,部分以较低的频率仅出现抗病或易感群体中。等位基因Scma-DBB1*04在抗病群体中出现频率为7%,而在易感群体中出现频率为42.9%,与易感性状相关(p=0.000);等位基因Scma-DBB2*01在抗病群体中出现频率为44.2%,而在易感群体中出现频率为19%,与抗病相关(p=0.013)相关。
Along with fast development of aquaculture, fish diseases occured frequently as the result of high breeding density and worsen environment. It is necessary to breed anti-pathogen stock for aquaculture development. The problems also need to be resolved for turtot, which is an important breeding fish in China. As MHC II B genes play a crucial role in innate and adaptive immune responses and a lot of evidences proved the association between different MHC II B alleles and resistance or susceptibility to pathogens. We studied the MHC polymorphism and association between alleles and resistance to Edwardsiella tarda here.
1. Characterization of turbot pathogen
Turbot pathogen- Edwardsiella tarda was characterized by 16S rDNA sequence analysis. The pathogen was islated from abdomen cavity as single clone during disease burst period and preserved in our lab. Part of 16S rDNA was amplified with 16S rDNA conserved primer 8F and 1492R of bacteria and sequenced. Three sequences with 1505bp length were obtained with small difference. High similarities were discovered with Edwardsiella ictaluri and Edwardsiella tarda by blast analysis in Genbank. Higher similarity with Edwardsiella tarda was revealed by phylogenetic tree analysis. And one of these sequenes, 16S rDNA-2, shared 100% similarity with Edwardsiella tarda via alignment analysis with Edwardsiella ictaluri and Edwardsiella tarda. Considering sequencing error and the difference of different copies of 16S rDNA, the pathogen of turbot was characterized as Edwardsiella tarda.
2. MHC II B polymorphism and associations with pathogen resistance in turbot
Four types of intron 1 were discovered, named as A, B, C and D, which were different at their length resulting from the repeats of a 19bp repeat element. There is a CT/GT rich region at 3` end of intron1, which is the potential site recognized by RecA, indicating that recombination might have happened.
59 alleles in total were discovered from 42 susceptible and 43 resistant individuals, including 35 of type A, 6 of type B, 13 of type C and 5 of type D. 25 of them were used to analyze distribution between resistant and susceptible stocks. Some alleles appeared in both susceptible and resistant stock with different frequency, while some only appeared in susceptible or resistant stock with low frequency. The allele Scma-DBB1*04 was discovered to be associated with susceptibility to Edwardsiella tarda with frequency 7% in resistant stock and 42.9% in susceptible (p=0.000). The allele Scma-DBB2*01 was associated with resistance, 44.2% in resistant stock and 19% in susceptible (p=0.013).
1.大菱鲆致病菌的鉴定
我们通过16S rDNA序列分析鉴定了大菱鲆致病菌-迟钝爱德华氏菌。该病原菌来自于实验室保存菌株,是在大菱鲆疾病暴发时期,从其腹腔内分离获取的单克隆。利用细菌16S rDNA保守区引物8F和1492R扩增其16S rDNA部分序列,并进行克隆测序。通过测序共获得1505bp的序列,所测三个转化子各不相同。将三条序列到Genbank上比对发现,其与两种细菌相似性最高:Edwardsiella ictaluri和Edwardsiella tarda。通过进化树分析可以发现,我们所得到的序列与Edwardsiella tarda亲缘关系最近,而与Edwardsiella ictaluri相差较远。并且其中一条序列16S rDNA-2与Edwardsiella ictaluri和Edwardsiella tarda序列比对时,其与Edwardsiella tarda有100%的相似度。考虑到细菌16S rDNA多拷贝间的差异以及测序误差在内,因此,可以将大菱鲆病原菌鉴定为迟钝爱德华氏菌(Edwardsiella tarda)。
2.大菱鲆MHC II B多态性及其与大菱鲆抗病力的关系
通过对大菱鲆MHC II B内含子1和外显子2的序列分析,共发现了4种不同的内含子1(A、B、C和D型),其不同是由于一19bp重复单元的重复次数不同所致。内含子1的3`端含有一个富含CT/GT的区,该区域为重组酶RecA的潜在识别位点,表明在其演化史中可能发生过重组事件。
通过对43个抗病个体中的224条序列和42个易感个体中的214条序列进行MHC II B外显子2分析,共发现了59个不同的等位基因,其中包括35个A型、6个B型、13个C型和5个D型。对其中的25个等位基因进行了抗病群体与易感群体的分布统计分析,部分等位基因在两个群体中都有分布,部分以较低的频率仅出现抗病或易感群体中。等位基因Scma-DBB1*04在抗病群体中出现频率为7%,而在易感群体中出现频率为42.9%,与易感性状相关(p=0.000);等位基因Scma-DBB2*01在抗病群体中出现频率为44.2%,而在易感群体中出现频率为19%,与抗病相关(p=0.013)相关。
Along with fast development of aquaculture, fish diseases occured frequently as the result of high breeding density and worsen environment. It is necessary to breed anti-pathogen stock for aquaculture development. The problems also need to be resolved for turtot, which is an important breeding fish in China. As MHC II B genes play a crucial role in innate and adaptive immune responses and a lot of evidences proved the association between different MHC II B alleles and resistance or susceptibility to pathogens. We studied the MHC polymorphism and association between alleles and resistance to Edwardsiella tarda here.
1. Characterization of turbot pathogen
Turbot pathogen- Edwardsiella tarda was characterized by 16S rDNA sequence analysis. The pathogen was islated from abdomen cavity as single clone during disease burst period and preserved in our lab. Part of 16S rDNA was amplified with 16S rDNA conserved primer 8F and 1492R of bacteria and sequenced. Three sequences with 1505bp length were obtained with small difference. High similarities were discovered with Edwardsiella ictaluri and Edwardsiella tarda by blast analysis in Genbank. Higher similarity with Edwardsiella tarda was revealed by phylogenetic tree analysis. And one of these sequenes, 16S rDNA-2, shared 100% similarity with Edwardsiella tarda via alignment analysis with Edwardsiella ictaluri and Edwardsiella tarda. Considering sequencing error and the difference of different copies of 16S rDNA, the pathogen of turbot was characterized as Edwardsiella tarda.
2. MHC II B polymorphism and associations with pathogen resistance in turbot
Four types of intron 1 were discovered, named as A, B, C and D, which were different at their length resulting from the repeats of a 19bp repeat element. There is a CT/GT rich region at 3` end of intron1, which is the potential site recognized by RecA, indicating that recombination might have happened.
59 alleles in total were discovered from 42 susceptible and 43 resistant individuals, including 35 of type A, 6 of type B, 13 of type C and 5 of type D. 25 of them were used to analyze distribution between resistant and susceptible stocks. Some alleles appeared in both susceptible and resistant stock with different frequency, while some only appeared in susceptible or resistant stock with low frequency. The allele Scma-DBB1*04 was discovered to be associated with susceptibility to Edwardsiella tarda with frequency 7% in resistant stock and 42.9% in susceptible (p=0.000). The allele Scma-DBB2*01 was associated with resistance, 44.2% in resistant stock and 19% in susceptible (p=0.013).
引文
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