Mason-Gamer Roberta J
Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.
BMC Evol Biol. 2007 Jun 14;7:92. doi: 10.1186/1471-2148-7-92.
Stowaway elements are short, non-autonomous DNA transposons categorized as miniature inverted-repeat transposable elements (MITEs). The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed. Thus, a phylogenetic perspective on presence vs. absence of elements in an aligned data set can provide valuable historical insights into the dynamics of MITE acquisition and loss.
A Stowaway-like element resides within the fourth intron of a beta-amylase gene in representatives of five genera in the wheat tribe, Triticeae. Its presence vs. absence was examined with reference to the beta-amylase gene tree topology, and in light of sequence comparisons of the beta-amylase elements to Triticeae Stowaway elements in the Entrez nucleotide database. Among the sequences lacking the element, there are five distinct putative excision footprints (one widespread and four restricted to unrelated lineages) and two flanking deletions. The sequences that do contain elements are polyphyletic on the beta-amylase tree, and their elements are divergent at the sequence level. The beta-amylase elements do not form a monophyletic group relative to other Stowaway elements in Entrez; most are more similar to elements from other loci in other Triticeae genomes than they are to one another.
Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway-like element has undergone multiple deletions from and insertions into the same site in beta-amylase intron 4 during the history of the tribe. The elements currently at the site represent multiple, distinct lineages that transcend generic boundaries. While patterns of Stowaway polymorphism across a phylogenetic data set do not allow evolutionary mechanisms to be inferred with certainty, they do provide insights into the dynamics of element evolution over an extended time scale. The historical perspective provided by a phylogenetic approach is complementary to the few studies in which ongoing MITE activity has been documented.
偷渡者元件是短的非自主DNA转座子，归类为微型反向重复转座元件（MITE）。禾本科植物基因组中MITE的高拷贝数表明其具有活跃的扩增和插入历史，但目前很少见到MITE的活性，从未观察到偷渡者元件的活性。因此，在比对数据集中从系统发育角度分析元件的存在与否，可以为MITE的获得和丢失动态提供有价值的历史见解。
在小麦族（Triticeae）五个属的代表中，一个类似偷渡者的元件位于β-淀粉酶基因的第四内含子中。根据β-淀粉酶基因树拓扑结构，并结合β-淀粉酶元件与Entrez核苷酸数据库中小麦族偷渡者元件的序列比较，研究了该元件的存在与否。在缺乏该元件的序列中，有五个不同的推定切除足迹（一个广泛存在，四个局限于不相关的谱系）和两个侧翼缺失。在β-淀粉酶基因树上，包含元件的序列是多系的，并且它们的元件在序列水平上存在差异。与Entrez中其他偷渡者元件相比，β-淀粉酶元件不形成单系类群；大多数元件与其他小麦族基因组中其他位点的元件相比，彼此之间的相似性更低。
综合系统发育分布、序列变异和Entrez数据库比较结果表明，在该族的历史中，一个类似偷渡者的元件在β-淀粉酶内含子4的同一位置经历了多次缺失和插入。目前位于该位置的元件代表了跨越属界限的多个不同谱系。虽然整个系统发育数据集中偷渡者多态性的模式无法确定推断进化机制，但它们确实为元件在较长时间尺度上的进化动态提供了见解。系统发育方法提供的历史视角与少数记录了当前MITE活性的研究互为补充。
