Schelkunov Mikhail I, Nuraliev Maxim S, Logacheva Maria D
Skolkovo Institute of Science and Technology, Moscow, Russia.
Institute for Information Transmission Problems, Moscow, Russia.
PeerJ. 2021 Aug 31;9:e12106. doi: 10.7717/peerj.12106. eCollection 2021.
The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species ( and ) and compared them to the transcriptomes of their close photosynthetic relatives ( sp., , and ). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
蛇菰科植物全都是失去了光合作用能力的物种。相反，它们通过寄生其他植物来获取养分。最近的研究表明，蛇菰科的质体基因组呈现出许多有趣的特征，其中最显著的一个特征是AT含量极高，接近90%。此外，蛇菰科质体基因组中的核苷酸替换率比其光合近缘物种高一个数量级，且没有松弛选择的迹象。目前，对于这些特征尚无确切解释。鉴于这些不寻常的特征，我们推测蛇菰科的核基因组在理解非光合植物的进化方面可能也会提供有价值的信息。为了深入了解这些基因组，在本研究中我们分析了两种蛇菰科植物（ 和 ）的转录组，并将它们与其近缘光合植物（ 属、 和 ）的转录组进行比较。我们的分析表明，蛇菰科核基因的AT含量与光合近缘物种没有显著差异。出于未知原因，蛇菰科基因中的核苷酸替换率比光合檀香目植物的基因高几倍；然而，蛇菰科中的负选择可能更强。我们观察到蛇菰科植物成员中与光合作用相关的基因大量丢失。此外，我们没有观察到几个其产物在质体基因组修复中起作用的基因的转录本。这意味着它们已经丢失或表达量极低，这可能解释了质体基因组中核苷酸替换率和AT含量的增加。
