Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae).
Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae).
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梨属（蔷薇科）Adh 和 LEAFY 的分子进化及其内含子的系统发育实用性
DOI：
10.1186/1471-2148-11-255
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发表时间：
2011-09-14
影响因子：
3.4
通讯作者：
Teng Y
中科院分区：
文献类型：
--
作者：
Zheng X;Hu C;Spooner D;Liu J;Cao J;Teng Y
梨属(Pyrus)属蔷薇科(Rosaceae)梨亚科(Maloideae)梨族，是我国重要的果树经济作物之一。梨属的系统发育尚未得到明确的重建。在我们以前的工作中，由于nrDNA阵列的不一致进化，内部转录间隔区(ITS)揭示了一种难以分辨的系统发育。因此，为了提高分辨率，本文对低拷贝核基因(LCNG)的内含子进行了探索。然而，在LCNGs的系统发育研究中应用LCNGs仍然是两个挑战，至少需要比较两个独立的核基因座。本研究选择LEAFY基因的第二内含子和乙醇脱氢酶基因(Adh)进行分子进化和系统发育研究。结果DNA序列分析揭示了梨和苹果、梨和苹果的adhgene基因具有复杂的同源和类同源结构。RT-PCR和基因组PCR的序列比较表明，一些粘附性同源物被认为是无功能的。对18个种的Adh1基因进行了部分序列测定，并鉴定出代表Adh1-1的3个亚对数。这导致了由于低序列分歧和假定的重组子的包含而导致分辨不佳的系统发育。对于LEAFY的第二内含子，LFY1int2和LFY2int2都发现了多个内含子，LFY1int2由于两个内含子的谱系分类而不足以进行系统发育分析，但LFY2int2-N表现出较高的序列差异，导致了最好的系统发育。这项研究记录了并列基因和非并列基因的共存，以及这些并列基因和同源基因的谱系分类。它揭示了可能导致错误的系统发育推断的重组体，并提出了使用LFY2int2-N改进的梨属的系统发育分辨率。结论本研究首次基于LCNGs对梨属进行了系统发育分析。古代和现代的重复导致了梨属和苹果属的副词和副词的复杂结构，导致了新的功能化、非功能化和可能的亚功能化。在所研究的所有同源基因中，LFY2int2-N是重建梨属系统发育的最好的核标记，因为LFY2int2-N具有合适的序列差异，并且没有进行谱系分类。
BackgroundThe genusPyrusbelongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny ofPyrushas not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron ofLEAFYand the alcohol dehydrogenase gene (Adh) were selected to investigate their molecular evolution and phylogenetic utility.ResultsDNA sequence analyses revealed a complex ortholog and paralog structure ofAdhgenes inPyrusandMalus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that someAdhhomologs are putatively nonfunctional. A partial region ofAdh1was sequenced for 18Pyrusspecies and three subparalogs representingAdh1-1were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron ofLEAFY, multiple inparalogs were discovered for bothLFY1int2andLFY2int2.LFY1int2is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs.LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution ofPyrususingLFY2int2-N.ConclusionsOur study represents the first phylogenetic analyses based on LCNGs inPyrus. Ancient and recent duplications lead to a complex structure ofAdhoutparalogs and inparalogs inPyrusandMalus, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs,LFY2int2-Nis the best nuclear marker for phylogenetic reconstruction ofPyrusdue to suitable sequence divergence and the absence of lineage sorting.
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DOI：
10.1111/j.1095-8339.1973.tb01734.x
发表时间：
1973-01-01
影响因子：
2.4
作者：
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通讯作者：
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影响因子：
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DOI：
10.1111/j.1095-8339.1996.tb00749.x
发表时间：
1996-06-01
影响因子：
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作者：
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