Biology subjects

Nuraliev, M. S.

Publications and source records attributed to Nuraliev, M. S..

3 recordsLinked to original sources

bioRxiv2025

The plastid genome of the non-photosynthetic plant Rhopalocnemis phalloides is one of the most polymorphic genomes known

The common ancestor of plants in the Balanophoraceae family lost the ability to photosynthesize, and all several dozen extant species of this family feed exclusively by parasitizing other plants. Previous studies have shown that the plastid genomes of Balanophoraceae present numerous unusual features, including an extraordinarily increased rate of mutation accumulation without an observable weakening of natural selection acting on the genes. This study aims to test the hypothesis that the increased rate of mutation accumulation could have led to exceptionally high levels of intraspecific polymorphism in Balanophoraceae. To this end, we studied the plastid genomes of 7 samples of the species Rhopalocnemis phalloides. Although all 7 plastid genomes possessed the same genes arranged in the same order, the level of polymorphism was indeed extremely high, possibly the highest among all known genomes of any living organisms. Specifically, the average genome-wide percent identity of the plastid genomes of Rhopalocnemis phalloides was 68.7%, and the average percent identity of the CDSs was 68.9%. Additionally, during this study, we discovered 60 taxonomically misclassified plastid genomes in NCBI databases; this result has independent value.

genomics↗

bioRxiv2020

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives.

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 shown that plastid genomes of Balanophoraceae have a number of interesting features, one of the most prominent of those being a tremendous AT content close to 90%. Also, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is greater by an order of magnitude compared to photosynthetic relatives, without signs of relaxed selection. All these features have no definite explanations. Given these unusual features, we supposed that it would be interesting to gain insight into the characteristics of nuclear genomes of Balanophoraceae. To do this, in the present study we analysed transcriptomes of two species from Balanophoraceae, namely Rhopalocnemis phalloides and Balanophora fungosa, and compared them with transcriptomes of their close photosynthetic relatives Daenikera sp., Dendropemon caribaeus, Malania oleifera. The analysis showed that the AT content of nuclear genes of Balanophoraceae does not markedly differ from that of photosynthetic relatives. The nucleotide substitution rate in genes of Balanophoraceae is for an unknown reason several times larger than in genes of photosynthetic Santalales, though the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in Balanophoraceae. Also, for Balanophoraceae we did not see transcripts of several genes whose products participate 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.

genomics↗

bioRxiv2018

Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their genomes, especially plastid genomes, markedly differ from the genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing on other plants. The genome is highly reduced (18 622 base pairs versus approximately 150 kilobase pairs in autotrophic plants) and possesses an outstanding AT content, 86.8%, the highest of all sequenced plant plastid genomes. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologues from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

genomics↗