Biotech and Omics Laboratory, Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Oman.
Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
Genes (Basel). 2020 Sep 25;11(10):1133. doi: 10.3390/genes11101133.
Chloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. and were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203-156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.
叶绿体是植物细胞中独特的细胞器，由于其进行光合作用的能力，负责维持地球上的生命形式。叶绿体中的多个功能基因负责发生在叶绿体中的各种代谢过程。考虑到它在维持地球上生命方面的基本作用，确定叶绿体基因组中的多样性水平、哪些基因和基因组内容已经丢失、哪些基因已转移到核基因组、重复事件以及叶绿体基因组的整体起源和进化非常重要。我们对 2511 个叶绿体基因组的分析表明，藻类叶绿体基因组的基因组大小和编码 DNA 序列（CDS）数量相对其他谱系较高。大约 10.31%的被检查物种在叶绿体基因组中丢失了跨越所有谱系的反向重复（IR）。全基因组分析揭示了寄生和异养植物中的 基因大约在 5600 万年前丢失。 和 被发现是藻类、苔藓植物、蕨类植物和裸子植物叶绿体基因组的特征标志基因；然而，在被子植物或木兰类植物的谱系中没有发现这些基因，它们大约在 203-156 万年前丢失了。在整个进化过程中，各种叶绿体编码基因在不同的物种谱系中丢失。然而， 基因被发现是叶绿体基因组中最稳定和完整的基因，在分析的任何物种中都没有丢失，这表明它是质体基因组的特征基因。我们的进化分析表明，叶绿体基因组起源于大约 1293 万年前的多个共同祖先，并在不同的分类谱系中经历了生动的重组事件。
