An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes.
An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes.
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DOI：
10.1186/1471-2164-10-45
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发表时间：
2009-01-23
期刊：
影响因子：
4.4
通讯作者：
Stougaard J
中科院分区：
文献类型：
--
作者：
Bertioli DJ;Moretzsohn MC;Madsen LH;Sandal N;Leal-Bertioli SC;Guimarães PM;Hougaard BK;Fredslund J;Schauser L;Nielsen AM;Sato S;Tabata S;Cannon SB;Stougaard J
大多数在农业上重要的豆科植物都属于蝶花科豆科的两个亚支系：Phaseoloids和Galegoids，它们大约在5千万年前分化。类相植物主要是热带植物，包括普通豆和大豆等作物。Galegoids大多是温带的，包括三叶草，蚕豆和模式豆类莲花和紫花苜蓿（两者都有大量的基因组测序）。相比之下，花生（arachhis hypogaea）属于黄檀类分支，黄檀类分支在凤蝶类分支中更为基础。这项工作的目的是整合花生与荷花和紫花苜蓿的遗传图谱，提高我们对花生基因组和豆科植物基因组的了解。为此，我们在Arachis图谱上放置了使用先前描述的生物信息学管道定义的比较锚点标记。此外，我们还研究了转座子在观察到的共音模式中的可能作用。花生的遗传图谱与荷花和紫花苜蓿基本一致，大多数合成块与每个基因组呈现单一的主要亲和力。这表明，最后一次共同的全基因组复制早于花生类从Galegoids和Phaseoloids中分化出来，共同的祖先基因组基本上是二倍体化的。这里进行的花生和模式豆科植物基因组比较，以及先前发表的荷花和紫花苜蓿的比较，使得所有可能的花生-荷花-紫花苜蓿物种间的比较得以进行，并观察到基因组的共系性。在所有的基因组比较中，都存在不同的保守的同源区和非保守区，这意味着某些豆类基因组区域在进化过程中始终比其他区域更稳定。我们发现，在紫花苜蓿中，也可能在莲花中，反转录转座子在可变区域更频繁。此外，虽然这些可变区域的单拷贝基因密度通常低于更保守的区域，但有些区域具有高密度的快速进化的抗病基因。我们认为，凤蝶的基因空间可以分为两个广泛定义的部分：更保守的区域往往具有较低的反转录转座子密度，并且在进化过程中相对稳定；可变区域往往具有较高的反转录转座子密度，其频繁的重组可能会促进某些基因家族的进化。
Most agriculturally important legumes fall within two sub-clades of the Papilionoid legumes: the Phaseoloids and Galegoids, which diverged about 50 Mya. The Phaseoloids are mostly tropical and include crops such as common bean and soybean. The Galegoids are mostly temperate and include clover, fava bean and the model legumes Lotus and Medicago (both with substantially sequenced genomes). In contrast, peanut (Arachis hypogaea) falls in the Dalbergioid clade which is more basal in its divergence within the Papilionoids. The aim of this work was to integrate the genetic map of Arachis with Lotus and Medicago and improve our understanding of the Arachis genome and legume genomes in general. To do this we placed on the Arachis map, comparative anchor markers defined using a previously described bioinformatics pipeline. Also we investigated the possible role of transposons in the patterns of synteny that were observed. The Arachis genetic map was substantially aligned with Lotus and Medicago with most synteny blocks presenting a single main affinity to each genome. This indicates that the last common whole genome duplication within the Papilionoid legumes predated the divergence of Arachis from the Galegoids and Phaseoloids sufficiently that the common ancestral genome was substantially diploidized. The Arachis and model legume genomes comparison made here, together with a previously published comparison of Lotus and Medicago allowed all possible Arachis-Lotus-Medicago species by species comparisons to be made and genome syntenies observed. Distinct conserved synteny blocks and non-conserved regions were present in all genome comparisons, implying that certain legume genomic regions are consistently more stable during evolution than others. We found that in Medicago and possibly also in Lotus, retrotransposons tend to be more frequent in the variable regions. Furthermore, while these variable regions generally have lower densities of single copy genes than the more conserved regions, some harbor high densities of the fast evolving disease resistance genes. We suggest that gene space in Papilionoids may be divided into two broadly defined components: more conserved regions which tend to have low retrotransposon densities and are relatively stable during evolution; and variable regions that tend to have high retrotransposon densities, and whose frequent restructuring may fuel the evolution of some gene families.
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DOI：
10.1093/dnares/dsn008
发表时间：
2008-08
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Sato S;Nakamura Y;Kaneko T;Asamizu E;Kato T;Nakao M;Sasamoto S;Watanabe A;Ono A;Kawashima K;Fujishiro T;Katoh M;Kohara M;Kishida Y;Minami C;Nakayama S;Nakazaki N;Shimizu Y;Shinpo S;Takahashi C;Wada T;Yamada M;Ohmido N;Hayashi M;Fukui K;Baba T;Nakamichi T;Mori H;Tabata S
通讯作者：
Tabata S
DOI：
10.1073/pnas.0402251101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Choi, HK;Mun, JH;Cook, DR
通讯作者：
Cook, DR
影响因子：
3
作者：
Seijo, Guillermo;Lavia, Graciela I.;Moscone, Eduardo A.
通讯作者：
Moscone, Eduardo A.
DOI：
10.1073/pnas.0605618103
发表时间：
2006-11-21
影响因子：
11.1
作者：
Vitte, Clementine;Bennetzen, Jeffrey L.
通讯作者：
Bennetzen, Jeffrey L.
影响因子：
4.4
作者：
Fredslund J;Madsen LH;Hougaard BK;Nielsen AM;Bertioli D;Sandal N;Stougaard J;Schauser L
通讯作者：
Schauser L