Centre for Ecology and Evolutionary Synthesis, Dept of Biology, University of Oslo, Norway.
BMC Genomics. 2010 Mar 5;11:154. doi: 10.1186/1471-2164-11-154.
We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA. A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region.
The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, ZAA. The IB region was extended with 350 kb including three new Z-lineage loci, ZBA, ZCA and ZDA in addition to a UGA locus. An allelic version of the IB region contained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previously known as UAA) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood.
Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene (UBA), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages.
我们之前已经对大西洋鲑鱼的 MHC Ⅰ类区域进行了超过 500kb 的测序。在 IA 区域，我们除了发现了一个可溶性 MHC Ⅰ类分子 Sasa-ULA 外，还鉴定出了 MHC Ⅰ类基因 Sasa-UBA 的基因座。在非经典的 IB 区域鉴定出了 Sasa-UCA 的假基因座。这两个区域都包含抗原呈递基因，以及与人类 MHC 区域内的其他基因的同源基因。
已确定了两种 MHC Ⅰ类谱系（Z 和 S）的基因组定位。使用标准 Sanger 和 454 测序相结合的方法对 7 个 BAC 进行了测序。新的序列数据扩展了 IA 区域 150kb，鉴定出了一个 Z 谱系基因座 ZAA 的位置。IB 区域扩展了 350kb，包括三个新的 Z 谱系基因座 ZBA、ZCA 和 ZDA，以及一个 UGA 基因座。除了假基因座 UCA 外，一个 IB 区域的等位基因版本还包含一个功能性 UDA 基因座。此外，一个含有两个 MHC Ⅰ类基因（UHA）的 BAC 被定位在连锁群 14 上，而一个含有 S 谱系基因座 SAA（以前称为 UAA）的 BAC 被定位在 LG10 上。基因表达研究表明，除了 UBA 在肠道、脾脏和鳃中高度表达，ZAA 在血液中高表达外，所有 MHC Ⅰ类基因的表达范围都很有限。
在这里，我们描述了大西洋鲑鱼的 U、Z 和 S 谱系的 MHC Ⅰ类基因座的基因组组织。描述的 9 个 MHC Ⅰ类基因位于重复的 IA 和 IB 区域的扩展部分，而 3 个 MHC Ⅰ类基因位于两个独立的连锁群上。这两个区域的基因组织表明，IB 区域的进化速度与 IA 区域不同。表达谱、多态性含量、肽结合特性和系统发育关系表明，大西洋鲑鱼除了拥有一个 MHC Ⅰ类基因（UBA）外，还有来自 U、S 和 Z 谱系的大量非经典 MHC Ⅰ类基因。
