F-box基因拷贝数目变异的机制研究：以12种果蝇为例

doi:10.3724/SP.J.1003.2011.14256

摘要/Abstract

摘要：

拷贝数目变异是一种对表型变异和生物进化具有重要意义的基因组结构变异。以前的研究表明不同物种中F-box基因的拷贝数目差异较大。为了深入探索拷贝数目变异的式样和机制, 我们以12个果蝇近缘种为研究对象, 分析了F-box基因的系统发育关系、进化式样以及它们在染色体上的位置。结果发现, 虽然各个物种中F-box基因的拷贝数目差别不大(42-47个), 但是仍然存在着很多引起拷贝数目变异的基因获得和丢失事件。这说明表面上变化不大的拷贝数目在一定程度上掩盖了频繁发生的基因获得和丢失事件。通过比较这些基因在染色体上的位置, 发现只有在亲缘关系很近的物种之间才能鉴定出有明显微共线性关系的基因组区段。我们还发现, 造成F-box基因拷贝数目增加的主要机制是散在重复和串联重复, 而反转录转座和新基因的非编码区起源也是两种值得注意的机制。此外, 序列变异导致的外显子边界变化以及外显子丢失是引起拷贝数目减少的两种机制。在12种果蝇的最近共同祖先中, F-box基因的拷贝数目与现存物种基本相似, 但是基因的获得和丢失事件使得现存物种中的F-box基因在构成上已经有了明显的差别。对数目变异的式样及其与基因功能的关系的研究表明, 拷贝数目变异是F-box基因家族“生与死”的进化在基因组层面的系统反映, 并有可能为表型变异提供了原始材料。

关键词: 拷贝数目变异, F-box基因, 果蝇, 直系同源基因

Abstract

Copy number variation (CNV) is a special type of mutational change that plays important roles in phenotypic variation and organismal evolution. To explore the mechanisms underlying copy number variation and to understand its biological significance, we analyzed the phylogenetic relationships, evolutionary patterns and chromosomal locations of F-box genes in 12 closely-related Drosophila species. A total of 541 F-box genes were identified and phylogenetic analyses suggested that they are members of 48 gene clusters (or orthologous groups). Although we observed no drastic changes in the total numbers of F-box genes among the 12 extant Drosophila species (42-47), we found many gene gain and loss events that have caused copy number variation. These results demonstrated that the similarity in the total numbers of F-box genes among different species has, to a certain degree, masked the frequent and independent gain and loss events. Comparisons of the chromosomal locations of orthologous genes showed that extensive microsynteny could be detected only between very closely-related sibling species. We also found that the main mechanisms that caused the increase in gene number were dispersed duplication and tandem duplication, while retroposition and de novo origination from non-coding sequences were two other noteworthy mechanisms. Mutations that caused shifts in exon-intron boundaries and/or losses of exons seemed to be the main mechanisms that underlie decreases in copy number. Although the most recent common ancestor (MRCA) of the 12 Drosophila species had a similar number of genes as the extant species we studied, gains of new genes and losses of existing ones have caused changes in the makeup of F-box genes in descendent species. Our study suggested that variations in the numbers of gene copies is a reflection of “birth-and-death” evolution at the genomic level and have provided raw materials for phenotypic and physiological diversification.

Key words: copy number variation, F-box gene, Drosophila, orthologs

李安, 徐桂霞, 孔宏智 (2011) F-box基因拷贝数目变异的机制研究：以12种果蝇为例. 生物多样性, 19, 3-16. DOI: 10.3724/SP.J.1003.2011.14256.

An Li, Guixia Xu, Hongzhi Kong (2011) Mechanisms underlying copy number variation in F-box genes: evidence from comparison of 12 Drosophila species. Biodiversity Science, 19, 3-16. DOI: 10.3724/SP.J.1003.2011.14256.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2011.14256

https://www.biodiversity-science.net/CN/Y2011/V19/I1/3

图/表 16

图1 果蝇12个近缘种的F-box基因的拷贝数目和对应的结构域组成。统计表的上方是果蝇12个近缘种的物种树(修改自 http://rana.lbl.gov/drosophila/index.html), 分支末端对应各自的物种名(用种名的前三个字母代替), 即拷贝数目统计表的第一行。统计表左侧是用48个直系同源基因分支中的代表序列构建的系统树, 各支末端对应统计表中该基因在12个物种中的拷贝数目; 右侧则为该基因编码的蛋白质的结构域组成模式图。灰色标出的行是有拷贝数目变异的基因。

Fig. 1 Copy number and domain structure of F-box proteins from 12 Drosophila species. The phylogenetic tree of the 12 Drosophila species (modified from http://rana.lbl.gov/drosophila/index.html) is above the table. The first three letters of each specific epithet are used as the abbreviation for each species. On the left side of the table is a neighbor-joining (NJ) tree for 48 clades of F-box proteins whose domain structure are shown on the right. Numbers in the table indicate the copy numbers of F-box genes belonging to each clade. Clades with copy number variations are shaded.

图2 F-box基因拷贝数目变异的典型情况。结构域的图例与图1的一致。A: 该基因在12个物种中均存在, 且在D. ananassae中又获得了一个拷贝; B: 该基因存在于10个物种中, D. yakuba和D. erecta的最近共同祖先丢失了这个基因; C: 该基因仅在D. mojavensis和D. virilis中存在, 说明此基因是在这两个物种的最近共同祖先中获得的; D: 物种树上部6个物种的最近共同祖先获得了该基因, 又在D. yakuba中发生丢失。E: 该基因在D. erecta、D. ananassae、D. willistoni和D. virilis这4个物种中分别丢失, 而在D. pseudoobscura和D. persimilis的最近共同祖先中发生了基因重复, 产生了第二个拷贝, 后来D. persimilis中的第一个拷贝丢失; F: 该基因在11个物种中存在, 在D. willistoni中丢失。物种树上部5个物种的最近共同祖先中增加了1个拷贝, 但D. melanogaster又丢掉了1个拷贝。

Fig. 2 Examples of copy number variation of F-box genes. Domain legends are the same as those in A, D. ananassae gained a new copy of F-box gene; B, The most recent common ancestor (MRCA) of D.yakuba and D.erecta lost the ortholog of Clade7; C, MRCA of D.mojavensisandD.virilis gained a new gene; D, MRCA of the top six species gained a new copy of F-box gene and D.yakuba lost this gene after their divergence; E, Four gene loss events occurred independently in D. erecta, D. ananassae, D. willistoni, and D. virilis. A gene duplication event happened in the MRCA of D.pseudoobscura and D.persimilis, generating two copies, but then one copy lost in D.persimilis; F, D.willistoni lost Clade24 gene. The MRCA of the top five species gained a new copy of this gene, but then D.melanogaster lost the new copy.

图3 F-box基因的拷贝数目在果蝇进化历史中的变化。圆圈和方框中的数字分别表示12个现存物种及其祖先中的拷贝数目。系统树分支上的+/-及数字表示基因拷贝数目的增减事件及增减的拷贝数目。系统发育树修改自Assembly/Alignment/ Annotation of 12 related Drosophila species [http://rana.lbl.gov/drosophila/index.html]。

Fig. 3 Evolutionary change of the copy number of F-box genes in Drosophila species. The numbers in circles and rectangles represent the copy numbers of genes in extant and ancestral species, respectively. Numbers above and below each branch indicate the numbers of gains (+) and losses (-) of genes, respectively. The phylogenetic tree is modified from Assembly/Alignment/Annotation of 12 related Drosophila species [http://rana.lbl.gov/drosophila/index.html].

图4 12个果蝇近缘种基因组中F-box基因的染色体定位及相互之间的直系同源与旁系同源关系。横向的长条表示12个果蝇的染色体臂/支架/片段。L和R分别指示染色体的左、右臂。五边形的黑色方块表示F-box基因。直系同源基因之间用直线相连, 实心圆圈表示基因重复事件。曲线表示其所穿过的染色体上已经丢失相应的直系同源基因。基因下面的数字代表其所在进化支的编号(粗体表示有拷贝数目变异的进化支)。由于这12个种的核型不同, 我们在D. melanogaster中将基因按从X染色体到3号染色体右臂的顺序展示, 并将其他物种的染色体按与D. melanogaster相对应的顺序排列。加粗的线指示了拷贝数目变异的三个例子。分别包括了一次获得(Clade22)、一次获得和一次丢失(Clade14)以及一次获得和两次丢失(Clade24)事件。

Fig. 4 Chromosomal locations of F-box genes and their orthologous and paralogous relationships in the 12 Drosophila genomes. Horizontal bars represent the chromosomal arms/scaffolds/segments of the 12 Drosophila genomes. L and R indicate the left and right arms of chromosomes, respectively. Hexagonal lumps designate F-box genes. Orthologs are connected by lines. Filled circles indicate gene duplication events. Orthologs connected by curve do not exist in the species between them. Numbers below genes are the No. of clades (those in bold indicate that the copy numbers are different among the 12 species). Since the 12 species are different in karyotype, we arranged the genes from chromosomes X to 3R in D. melanogaster, and the chromosomes in other species are arranged corresponding to D. melanogaster. Lines in bold indicate three examples of copy number variation, which show one gain (Clade22), one gain and one loss (Clade14), as well as one gain and two losses (Clade24), respectively.

图5 F-box基因拷贝数目变异的机制。A: Clade22拷贝数目增加的机制是反转录转座。(a)旁系同源基因的结构比较(祖先状态在上)。细线连接具有较高序列一致性的部分, 数字表示该部分的长度。(b)该无内含子的F-box基因(下划线且粗体)有一个类似poly-A尾巴(灰色)的结构和两段正向重复序列(框内)。B: Clade18拷贝数目增加的机制是从头起源。新基因起源于CG1792和pasha(D. melanogaster中的名字)两基因之间的非编码序列。(c)和(d)是该F-box基因与前述非编码序列的比对示意图(详见附录V)。C: F-box基因拷贝数目减少的机制。图示直系同源基因之间的结构比较(祖先状态在上)。

Fig. 5 Mechanisms for copy number variation of F-box genes. A, The mechanism that caused the increase in copy number of Clade22 was retroposition. (a) Comparison of the exon/intron structure of paralogs is showed (the upper gene is similar to ancestral gene). Regions that can match to each other are connected with thin lines, and the numbers show the length of the matched parts. (b) The intronless F-box gene (underlined and in bold) likely possesses a poly-A tail (in gray) and two direct repeats (in boxes). B, The mechanism that caused the increase in copy number of Clade18 was de novo origination. The new gene was derived from non-coding sequences between CG1792 and pasha (respectively named after orthologous genes in D. melanogaster). (c) and (d) are alignments between non-coding sequences and F-box genes (Appendix V for the details). C, Mechanisms for the decrease in copy number of F-box genes. Comparison of the exon/intron structures between orthologs are showed (the upper gene is ancestral).

附录I 冗余序列的筛选列表

Appendix I Redundant sequences and the one finally selected

冗余序列 Redundant sequences	所选的序列 Selected sequences
FBpp0073103, FBpp0073101, FBpp0073102	FBpp0073102
FBpp0078592, FBpp0110535, FBpp0078594, FBpp0078593	FBpp0078593
FBpp0084796, FBpp0084795	FBpp0084795
FBpp0110196, FBpp0078693	FBpp0078693
FBpp0087190, FBpp0111982, FBpp0111980, FBpp0111981	FBpp0111981
FBpp0086875, FBpp0086876	FBpp0086876
FBpp0087274, FBpp0087275, FBpp0087276	FBpp0087276
FBpp0083216, FBpp0083215	FBpp0083215
FBpp0099839, FBpp0099383	FBpp0099383
FBpp0268227, FBpp0264637	FBpp0264637
FBpp0259602, FBpp0267478	FBpp0267478
FBpp0267102, FBpp0267103	FBpp0267103
FBpp0153606, FBpp0157663	FBpp0157663
FBpp0157330, FBpp0144755	FBpp0144755
FBpp0157205, FBpp0157374	FBpp0157374

附录II 重新注释的基因

Appendix II Re-annotated genes

重新注释的基因 Re-annotated genes	对应的蛋白质 Corresponding proteins
Dsim\GD12690	FBpp0211092
Dmel\CG14102	FBpp0074697
Dyak\GE20089	FBpp0265099
Dpse\GA21694	FBpp0280727

附录III 果蝇的12个近缘种中F-box蛋白质的系统发育关系。树中基因的名字用对应的物种的种加词前3个字母、蛋白质序列名和该蛋白质的C端结构域组成(其中N即none)。

Appendix III Phylogenetic tree of F-box proteins from 12 Drosophila species. The name of each protein is composed of the first three letters of the specific epithet, followed by the name of the sequence and the C-terminal domain (N means none).