Patterns of selective constraints in noncoding DNA of rice.
Patterns of selective constraints in noncoding DNA of rice.
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DOI：
10.1186/1471-2148-7-208
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发表时间：
2007-11-01
影响因子：
3.4
通讯作者：
Fan L
中科院分区：
文献类型：
--
作者：
Guo X;Wang Y;Keightley PD;Fan L
一些研究已经调查了内含子中的选择性限制与它们的长度、GC含量和在基因内的位置之间的关系。然而，到目前为止，还没有在植物中进行过这样的研究。在非编码DNA的选择性约束的研究通常涉及种间比较，假设相同的选择压力作用于每个谱系。这样的比较仅限于非编码序列不太强烈发散的情况，从而可以获得可靠的序列比对。在这里，我们研究了最近的片段重复中的选择性限制，其中包括大约700万年前在水稻中发生的605个旁系同源内含子对（O。sativa）。我们的主要发现是：（1）内含子分歧与内含子长度负相关，这是先前在果蝇和哺乳动物中描述的模式;（2）在剪接控制位点处存在强纯化选择的特征;（3）第一内含子比其他内含子显著更长并且具有更高的GC含量;（4）第一内含子和非第一内含子的分歧彼此没有显著差异，这一模式不同于果蝇和哺乳动物;（5）短内含子比四重简并位点更加趋异，表明选择减少了四重位点的趋异。我们观察到较强的选择性限制在长的内含子表明，功能元件的纯化选择可能集中在长的内含子。我们的结果是一致的存在下，强大的纯化选择剪接控制网站。与其他物种不同，水稻第一内含子的选择性限制并不明显更强。
Several studies have investigated the relationships between selective constraints in introns and their length, GC content and location within genes. To date, however, no such investigation has been done in plants. Studies of selective constraints in noncoding DNA have generally involved interspecific comparisons, under the assumption of the same selective pressures acting in each lineage. Such comparisons are limited to cases in which the noncoding sequences are not too strongly diverged so that reliable sequence alignments can be obtained. Here, we investigate selective constraints in a recent segmental duplication that includes 605 paralogous intron pairs that occurred about 7 million years ago in rice (O. sativa). Our principal findings are: (1) intronic divergence is negatively correlated with intron length, a pattern that has previously been described in Drosophila and mammals; (2) there is a signature of strong purifying selection at splice control sites; (3) first introns are significantly longer and have a higher GC content than other introns; (4) the divergences of first and non-first introns are not significantly different from one another, a pattern that differs from Drosophila and mammals; and (5) short introns are more diverged than four-fold degenerate sites suggesting that selection reduces divergence at four-fold sites. Our observation of stronger selective constraints in long introns suggests that functional elements subject to purifying selection may be concentrated within long introns. Our results are consistent with the presence of strong purifying selection at splicing control sites. Selective constraints are not significantly stronger in first introns of rice, as they are in other species.
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影响因子：
7
作者：
Halligan, DL;Eyre-Walker, A;Keightley, PD
通讯作者：
Keightley, PD
影响因子：
3.5
作者：
Guo, Xingyi;Bao, Jiandong;Fan, Longjiang
通讯作者：
Fan, Longjiang
DOI：
10.1073/pnas.052139599
发表时间：
2002-04-30
影响因子：
11.1
作者：
Kaplinsky, NJ;Braun, DM;Freeling, M
通讯作者：
Freeling, M
DOI：
10.1002/jez.b.21122
发表时间：
2007-01-15
影响因子：
2.2
作者：
Jiang, Huifeng;Liu, Dongyuan;Wang, Wen
通讯作者：
Wang, Wen
影响因子：
7
作者：
Inada, DC;Bashir, A;Freeling, M
通讯作者：
Freeling, M