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首页> 外文期刊>Genomics >Songbird genomics: analysis of 45 kb upstream of a polymorphic Mhc class II gene in red-winged blackbirds (Agelaius phoeniceus).
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Songbird genomics: analysis of 45 kb upstream of a polymorphic Mhc class II gene in red-winged blackbirds (Agelaius phoeniceus).

机译：鸣禽基因组学：分析红翅黑鸟（Agelaius phoeniceus）的Mhc II类多态基因上游45 kb。

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摘要

Here we present the sequence of a 45 kb cosmid containing a previously characterized poly-morphic Mhc class II B gene (Agph-DAB1) from the red-winged blackbird (Agelaius phoeniceus). We compared it with a previously sequenced cosmid from this species, revealing two regions of 7.5 kb and 13.0 kb that averaged greater than 97% similarity to each another, indicating a very recent shared duplication. We found 12 retroelements, including two chicken repeat 1 (CR1) elements, constituting 6.4% of the sequence and indicating a lower frequency of retroelements than that found in mammalian genomic DNA. Agph-DAB3, a new class II B gene discovered in the cosmid, showed a low rate of polymorphism and may be functional. In addition, we found a Mhc class II B gene fragment and three genes likely to be functional (encoding activin receptor type II, a zinc finger, and a putative gamma-filamin). Phylogenetic analysis of exon 2 alleles of all three known blackbird Mhc genes indicated strong clustering of alleles by locus, implying that large amounts of interlocus gene conversion have not occurred since these genes have been diverging. Despite this, interspecific comparisons indicate that all three blackbird Mhc genes diverged from one another less than 35 million years ago and are subject to concerted evolution in the long term. Comparison of blackbird and chicken Mhc promoter regions revealed songbird promoter elements for the first time. The high gene density of this cosmid confirms similar findings for the chicken Mhc, but the segment duplications and diversity of retroelements resembles mammalian sequences.
机译：在这里，我们介绍了一个45 kb粘粒的序列，该粘粒包含来自红翅黑鸟（Agelaius phoeniceus）的先前表征的Mhc II B类多态性基因（Agph-DAB1）。我们将其与该物种先前测序的粘粒进行了比较，揭示了两个7.5 kb和13.0 kb的区域，它们彼此之间的平均相似度大于97％，这表明它们之间存在着最近的重复。我们发现了12个逆转录元素，包括两个鸡重复序列1（CR1）元素，构成序列的6.4％，表明逆转录因子的频率比在哺乳动物基因组DNA中更低。 Agph-DAB3是一种在粘粒中发现的新的II B类基因，其多态性率较低，可能具有功能。此外，我们发现了Mhc II B类基因片段和三个可能起作用的基因（编码激活素受体II型，锌指和推定的γ-丝氨酸）。对所有三个已知的黑鸟Mhc基因的外显子2等位基因的系统发生分析表明，等位基因通过位点强烈聚集，这表明自这些基因发散以来，尚未发生大量中间基因转换。尽管如此，种间比较表明，所有三个黑鸟Mhc基因在不到3500万年前就彼此分开，并且长期处于协调一致的进化过程中。黑鸟和鸡Mhc启动子区域的比较首次揭示了鸣鸟启动子元件。这种粘粒的高基因密度证实了鸡Mhc的类似发现，但是节段重复和反转录元件的多样性与哺乳动物序列相似。

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