Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage
Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage
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DOI：
10.1093/molbev/msq229
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发表时间：
2011-01-01
影响因子：
10.7
通讯作者：
Jansen, Robert K.
中科院分区：
文献类型：
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作者：
Guisinger, Mary M.;Kuehl, Jennifer V.;Jansen, Robert K.
老鹳草科质体基因组（质体）经历了显着数量的基因组变化。本文对毛茛、掌叶老鹳草和Monsonia speciosa的质体进行了测序，并与其它蔷薇科植物和先前发表的天竺葵质体进行了比较。天竺葵科质体被发现是高度可变的大小，基因内容和顺序，重复DNA，和密码子使用。几种独特的质体重组包括两个高度保守的操纵子（S10和rps 2-atpA）的破坏，以及M中的反向重复（IR）区域。speciosa不包含核糖体RNA操纵子中的所有基因。M. speciosa是不寻常的小（128，787 bp）;在被子植物质体测序的日期，只有那些非光合物种和那些失去了一个IR拷贝较小。相比之下，P. hortorum的质体组最大，为217，942 bp。这些基因组经历了大量的基因和内含子丢失以及部分和完全的基因复制。有些损失是由整个家庭分担的（例如，trnT-GGU以及rps 16和rpl 16的内含子）;然而，其它丢失是同源的（例如，trnG-UCC内含子存在于G. palmatum和M. speciosa）。IR长度也高度可变。以前在P. hortorum中的IR被证明大大扩展到76 kb，而在E. texanum和G. palmatum（11 kb）和M. speciosa（7 kb）.相对于其它蔷薇科植物，老鹳草科质体含有高频率的大重复序列（> 100 bp）。在每个质体组内，重复序列通常位于重排终点，并且许多重复序列在四个牛儿草科侧翼重排终点之间共享。GC含量在基因组中升高，并且相对于其他蔷薇科植物在编码区中也升高。每个氨基酸的密码子使用和GC含量在第三个位置的网站是显着不同的老鹳草科蛋白质编码序列相对于其他蔷薇科。我们的研究结果表明，宽松的选择和/或突变的偏见导致GC含量增加，这反过来又改变了密码子的使用。我们认为基因组重排、重复DNA、核苷酸替换和GC含量的增加可能是由于DNA修复不当导致的放松选择造成的。
Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be highly variable in size, gene content and order, repetitive DNA, and codon usage. Several unique plastome rearrangements include the disruption of two highly conserved operons (S10 and rps2-atpA), and the inverted repeat (IR) region in M. speciosa does not contain all genes in the ribosomal RNA operon. The sequence of M. speciosa is unusually small (128,787 bp); among angiosperm plastomes sequenced to date, only those of nonphotosynthetic species and those that have lost one IR copy are smaller. In contrast, the plastome of P. hortorum is the largest, at 217,942 bp. These genomes have experienced numerous gene and intron losses and partial and complete gene duplications. Some of the losses are shared throughout the family (e.g., trnT-GGU and the introns of rps16 and rpl16); however, other losses are homoplasious (e.g., trnG-UCC intron in G. palmatum and M. speciosa). IR length is also highly variable. The IR in P. hortorum was previously shown to be greatly expanded to 76 kb, and the IR is lost in E. texanum and reduced in G. palmatum (11 kb) and M. speciosa (7 kb). Geraniaceae plastomes contain a high frequency of large repeats (> 100 bp) relative to other rosids. Within each plastome, repeats are often located at rearrangement end points and many repeats shared among the four Geraniaceae flank rearrangement end points. GC content is elevated in the genomes and also in coding regions relative to other rosids. Codon usage per amino acid and GC content at third position sites are significantly different for Geraniaceae protein-coding sequences relative to other rosids. Our findings suggest that relaxed selection and/or mutational biases lead to increased GC content, and this in turn altered codon usage. We propose that increases in genomic rearrangements, repetitive DNA, nucleotide substitutions, and GC content may be caused by relaxed selection resulting from improper DNA repair.