Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.

中文翻译：

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西番莲猖Nuclear的核转移和质体基因的替代。

质体基因组（质体组）中的基因损失通常伴随着功能转移到细胞核或替代性的核编码基因的替代。尽管光合陆地植物的质体组中基因的保守程度很高，但最近的基因损失事件已在几个不同的被子植物进化枝中被记录下来。在这些谱系中，西番莲缺少几个必需的核糖体基因rps7，rps16，rpl20，rpl22和rpl32，这两个最大的质体基因ycf1和ycf2，并且具有高度不同的rpoA。比较转录组分析来确定西番莲缺失基因的命运。的推定的功能性转移RPS7，RPL22，和RPL32检测到细胞核，与的核转移RPS7，较被子植物一种新颖的事件。将质体编码的rps7转移到核编码质体靶向的硫氧还蛋白m型基因的内含子中，获得其质体转运肽（TP）。质体rpl20可能经历了重复的，核编码的线粒体靶向rpl20的新型取代具有相似的基因结构。此外，蔷薇类植物中，对于第三个独立转移证据RPL22在西番莲中检测到从含有细胞器RNA识别基序的核基因获得了TP。核成绩单代表rpoA，ycf1和ycf2没有被发现。进一步的分析表明，不同的rpoA仍然起作用，并且该基因在不同进化枝中处于阳性或纯化选择之下。对比分析表明，替代易位子和马达蛋白质复合物可以具有取代的损失ycf1和ycf2在西番莲。