The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula.
The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula.
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DOI：
10.1186/1471-2229-8-133
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发表时间：
2008-12-23
影响因子：
5.3
通讯作者：
Lee SH
中科院分区：
文献类型：
--
作者：
Shin JH;Van K;Kim DH;Kim KD;Jang YE;Choi BS;Kim MY;Lee SH
大豆脂氧合酶（Lxs）在植物抗性和赋予大豆独特风味中起着重要作用。Lxs包含一个多基因家族，包括GmLx1， GmLx2和GmLx3，其中许多基因已经被表征。由于大豆经历了两轮多倍体，我们对从进化角度研究大豆脂氧合酶同工酶之间的关系感兴趣。本文报道了古代和近代多倍体产生的大豆Lx区四分体基因组结构。同时，对大豆和紫花苜蓿共同祖先的Lxs进行了比较基因组学分析。分析了苜蓿中与大豆具有同源性的两个Lx区。通过观察大豆和紫花苜蓿的差异进化率，确定Mt-Mt、Gm-Mt和Gm-Gm亲缘关系的Ks中值分别为0.75、0.62和0.46。因此，Gm-Mt同源物（Ks = 0.62）和Gm-Mt同源物（Ks = 0.45）的比较支持了在Medicago-Glycine分裂之前共同祖先中Lx区域的古代重复。物种形成后，在紫花苜蓿中未发现其他多倍体产生的Lx区。相反，观察到Lx基因的串联重复。另一方面，大豆发生了谱系特异性重复，导致两对Lx区域。每对大豆区域与Medicago的一个Lx区域同源。通过系统发育分析，将34个Lx基因（15个MtLxs和19个GmLxs）分为两组。我们的研究表明，Lx基因家族是从最近的共同祖先的两个不同的Lx基因进化而来的。本研究分析了大豆两轮多倍体产生的两对Lx区域。每一对大豆同源区域都与紫花苜蓿的一个区域共同源，表明大豆基因组的四重奏结构。大豆和紫花苜蓿的进化速率存在差异；因此，对于每种比较情况：大豆-大豆、大豆-紫花苜蓿或紫花苜蓿-紫花苜蓿，应采用最佳的k /年速率，以准确估计聚结时间。结果表明，大豆Lx基因家族在分类单元分化前先发生了古老的多倍体扩增，随后分别发生了大豆特异性重复和串联重复。
Soybean lipoxygenases (Lxs) play important roles in plant resistance and in conferring the distinct bean flavor. Lxs comprise a multi-gene family that includes GmLx1, GmLx2 and GmLx3, and many of these genes have been characterized. We were interested in investigating the relationship between the soybean lipoxygenase isozymes from an evolutionary perspective, since soybean has undergone two rounds of polyploidy. Here we report the tetrad genome structure of soybean Lx regions produced by ancient and recent polyploidy. Also, comparative genomics with Medicago truncatula was performed to estimate Lxs in the common ancestor of soybean and Medicago. Two Lx regions in Medicago truncatula showing synteny with soybean were analyzed. Differential evolutionary rates between soybean and Medicago were observed and the median Ks values of Mt-Mt, Gm-Mt, and Gm-Gm paralogs were determined to be 0.75, 0.62, and 0.46, respectively. Thus the comparison of Gm-Mt paralogs (Ks = 0.62) and Gm-Mt orthologs (Ks = 0.45) supports the ancient duplication of Lx regions in the common ancestor prior to the Medicago-Glycine split. After speciation, no Lx regions generated by another polyploidy were identified in Medicago. Instead tandem duplication of Lx genes was observed. On the other hand, a lineage-specific duplication occurred in soybean resulting in two pairs of Lx regions. Each pair of soybean regions was co-orthologous to one Lx region in Medicago. A total of 34 Lx genes (15 MtLxs and 19 GmLxs) were divided into two groups by phylogenetic analysis. Our study shows that the Lx gene family evolved from two distinct Lx genes in the most recent common ancestor. This study analyzed two pairs of Lx regions generated by two rounds of polyploidy in soybean. Each pair of soybean homeologous regions is co-orthologous to one region of Medicago, demonstrating the quartet structure of the soybean genome. Differential evolutionary rates between soybean and Medicago were observed; thus optimized rates of Ks per year should be applied for accurate estimation of coalescence times to each case of comparison: soybean-soybean, soybean-Medicago, or Medicago-Medicago. In conclusion, the soybean Lx gene family expanded by ancient polyploidy prior to taxon divergence, followed by a soybean- specific duplication and tandem duplications, respectively.
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影响因子：
3.9
作者：
Fuller, MA;Weichert, H;Grimes, HD
通讯作者：
Grimes, HD
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56.9
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