Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium.
Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium.
Curr Biol. 2017 Dec 18;27(24):3771-3782.e6. doi: 10.1016/j.cub.2017.11.004. Epub 2017 Nov 30.
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
几乎所有的质体（叶绿体）基因组都是圆形的双链 DNA 分子，大小通常在 100 到 200 kb 之间，编码约 80-250 个基因。这种普遍的质体基因组结构也有一些例外，例如甲藻，其基因位于 DNA 小环上。在这里，我们报告了绿藻 Cladophorales 的高度异常的叶绿体基因组，它完全碎片化为发夹染色体。通过对 DNA 和 RNA 的短读长和长读长高通量测序表明，Boodlea composita 的叶绿体基因编码在 1-7kb 的 DNA 连续体上，具有异常高的 GC 含量，每个连续体都包含一个长的反向重复序列，其中包含一个或两个编码蛋白质的基因和保守的非编码区域，可能涉及复制和/或表达。我们提出这些连续体对应于线性单链 DNA 分子，它们自身折叠形成发夹染色体。Boodlea 的叶绿体基因与其相应的同源基因高度不同，并且显示出替代的遗传密码。这种高度异常的叶绿体基因组的起源很可能发生在 Cladophorales 出现之前，并且与叶绿体基因向细胞核的大量转移同时发生。由线性 DNA 分子组成的叶绿体基因组在真核生物中是前所未有的，突出了质体基因组结构的意想不到的变化。
