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Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales. | LitMetric

Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales.

BMC Genomics

Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.

Published: November 2022

AI Article Synopsis

  • The study analyzed and compared the mitochondrial genomes of three Primula species, revealing structural variations and a high level of nucleotide diversity within the group and between regions like the Mediterranean and Himalaya-Hengduan Mountains.
  • Findings indicated that RNA editing events, particularly in the atp6 gene, were significant and conserved across Ericales, helping clarify evolutionary relationships within the family and among Primula species.
  • The research highlighted potential factors influencing mitogenome size, such as the transfer of mitochondrial plastid sequences and foreign DNA, although these connections remained largely insignificant overall.

Article Abstract

Background: Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales.

Results: Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall.

Conclusions: The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9686101PMC
http://dx.doi.org/10.1186/s12864-022-08983-xDOI Listing

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