Distribution of nuclear mitochondrial pseudogenes in three pollinator fig wasps associated with Ficus pumila
Distribution of nuclear mitochondrial pseudogenes in three pollinator fig wasps associated with Ficus pumila
复制标题
与榕相关的三种传粉无花果黄蜂核线粒体假基因的分布
DOI：
10.1016/j.actao.2013.10.001
复制
发表时间：
2014-05-01
影响因子：
1.8
通讯作者：
Chen, Xiao-Yong
中科院分区：
文献类型：
--
作者：
Chen, Yan;Liu, Min;Chen, Xiao-Yong
核线粒体假基因（NUMTs）是从线粒体基因组转移的核序列。虽然分布广泛，但它们在种群或近缘种中的分布模式很少有文献记载。利用直接测序和克隆测序的方法，对中国东南部3种为无花果（Ficus pumila, Wiebesia sp. 1、2和3）授粉的无花果黄蜂进行了线粒体细胞色素b （Cytb）基因扩增和测序，以检测其numt基因。通过直接测序，获得了33个单倍型的332个长度为487 bp的明确序列。它们的分布与细胞色素c氧化酶I亚基（COI）的分布高度一致。numt的不均匀分布表明它们有明显的共扩增迹象。12个威伯氏菌3号种群和3个威伯氏菌北部种群的13个个体均检测到numt，潜在共扩增产物测序克隆证实为numt。这些NUMT要么聚集为基于mtDNA Cytb分支的NUMT分支（基础NUMT），要么与Cytb单倍型一起聚集。基础numt具有终止密码子或106 bp片段缺失导致的移帧突变。此外，在每个NUMT分支中没有检测到第三个密码子或同义替换。系统发育树显示，在三个物种分化之前，基础numt已插入细胞核。在它们的第三密码子替换率上没有发现显著的两两差异，这表明这些numt起源于一次转移事件，核基因组中的重复导致了381 bp拷贝的共存。Cytb单倍型与与Cytb单倍型聚集的numt之间没有明显的替代差异。然而，这些NUMT单倍型在多个种群中与Cytb单倍型共存，这表明这些NUMT单倍型是最近插入核基因组的。基部和最近插入的numt都是罕见的事件，并且在大多数种群中不存在。需要进一步的研究来区分产生这种罕见性的潜在机制，如净化选择、遗传漂变或扩增失败。(c) 2013年Elsevier Masson SAS。版权所有。
Nuclear mitochondrial pseudogenes (NUMTs) are nuclear sequences transferred from mitochondrial genomes. Although widespread, their distribution patterns among populations or closely related species are rarely documented. We amplified and sequenced the mitochondrial cytochrome b (Cytb) gene to check for NUMTs in three fig wasp species that pollinate Ficus pumila (Wiebesia sp. 1, 2 and 3) in Southeastern China using direct and cloned sequencing. Unambiguous sequences (332) of 487 bp in length belonging to 33 haplotypes were found by direct sequencing. Their distribution was highly concordant with those of cytochrome c oxidase subunit I (COI). Obvious signs of co-amplification of NUMTs were indicated by their uneven distribution. NUMTs were observed in all individuals of 12 populations of Wiebesia sp. 3, and 13 individuals of three northern populations of Wiebesia sp. I. Sequencing clones of potential co-amplification products confirmed that they were NUMTs. These NUMTs either clustered as NUMT clades basal to mtDNA Cytb clades (basal NUMTs), or together with Cytb haplotypes. Basal NUMTs had either stop codons or frame-shifting mutations resulting from deletion of a 106 bp fragment. In addition, no third codon or synonymous substitutions were detected within each NUMT clade. The phylogenetic tree indicated that basal NUMTs had been inserted into nuclei before divergence of the three species. No significant pairwise differences were detected in their ratios of third codon substitutions, suggesting that these NUMTs originated from one transfer event, with duplication in the nuclear genome resulting in the coexistence of the 381 bp copy. No significant substitution differences were detected between Cytb haplotypes and NUMTs that clustered with Cytb haplotypes. However, these NUMTs coexisted with Cytb haplotypes in multiple populations, suggesting that these NUMT haplotypes were recently inserted into the nuclear genome. Both basal and recently inserted NUMTs were rare events, and were absent in most populations of Wiebesia sp. 1 and 2. Further studies are needed to distinguish between mechanisms potentially generating this rarity, such as purifying selection, genetic drift or amplification failure. (c) 2013 Elsevier Masson SAS. All rights reserved.