The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

Kan, Shenglong; Shen, Tingting; Gong, Ping; Ran, Jin-Hua; Wang, Xiaoquan

doi:10.1186/s12862-020-1582-1

Cited by 59 publications

(81 citation statements)

References 94 publications

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“…As part of the genome annotation process, we inferred RNA editing sites for protein-coding genes. The number of RNA editing sites predicted by PREP-Mt for the protein-coding genes of the Siberian larch mitogenome was within the range predicted with the same cut-off 0.2 in other gymnosperms, but varied greatly between different species from 225 in Welwitschia to 1102 in Taxus, 1179 in Pinus, 1206 in Cycas, and 1306 in Ginkgo (see Table 1 in [34]. The number of RNA editing sites correlated neither with mitogenome size nor with GC content, but more data are needed to make stronger conclusions.…”

Section: Discussionmentioning

confidence: 52%

“…The reasons for extremely large size of mitogenomes in plants are still not fully understood, but at least can be partly explained by a variable number of mobile genetic elements, introns and plasmid-related sequences [51] and could be affected by different factors, such as proliferation of retrotransposons, generation of repetitive DNA by recombination, and transferring of foreign sequences from plastid or nuclear genomes or via horizontal exchange of mitochondrial DNA (see [34] for discussion). However, it is unlikely that plasmids contributed much into the Siberian larch mitogenome size as we found relatively few plasmid-like insertions, representing only 0.11% of the entire mitogenome.…”

Section: Discussionmentioning

confidence: 99%

“…However, there are still very little published comparative mitogenome studies in gymnosperms, one of the oldest among the major plant clades comprising 14 families with more than 1000 species. Among all plant mitochondria genomes available, few gymnosperm mitogenomes have been fully assembled and properly annotated: Cycas taitungensis (415 Kbp) [32], a ginkgo tree Ginkgo biloba (347 Kbp) [33], a gnetophyte Welwitschia mirabilis (979 Kbp) [33], the Japanese yew Taxus cuspidata (469 Kbp) [34] and six conifer species (the Pinaceae family), such as white spruce -Picea glauca (5.9 Mbp) [35], Norway spruce -Picea abies (4.3 Mbp [36] In this study, we report on the sequencing, assembly, and annotation of the mitogenome of Siberian larch, a key species for the Siberian boreal forest and ecosystem.…”

Section: Introductionmentioning

confidence: 99%

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Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

et al. 2020

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Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

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Section: Discussionmentioning

confidence: 52%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

et al. 2020

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“…Most angiosperm mt genomes contain 24 to 41 protein coding genes, three rRNA genes, and two or three rRNA genes [ 2 , 3 , 4 , 5 , 6 , 7 ]. Recent mitochondrial genome studies have demonstrated horizontal gene transfer (HGT) and intracellular gene transfer (IGT) [ 5 , 8 , 9 , 10 , 11 ]. Additionally, plant mitochondria contain mitochondrial-encoded cytoplasmic male sterility (CMS) genes, which are related to the production of functional pollen or functional male reproductive organs [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS)

Choi

Park

2021

IJMS

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Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respectively. The chloroplast genome of A. indica shows massive plastid genes and the loss of one IR (inverted repeat). A comparison of the A. indica chloroplast genome sequence with that of a previous study demonstrated that the two chloroplast genomes encode a similar number of proteins (except atpH) but differ greatly in length. The A. indica mitochondrial genome has 53 genes, including 35 protein-coding genes (34 native mitochondrial genes and one chloroplast gene), 15 tRNA (11 native mitochondrial genes and four chloroplast genes) genes, and three rRNA genes. Evidence for intracellular gene transfer (IGT) and horizontal gene transfer (HGT) was obtained for plastid and mitochondrial genomes. ψndhB and ψcemA in the A. indica mitogenome were transferred from the plastid genome of A. indica. The atpH gene in the plastid of A. indica was transferred from another plastid angiosperm plastid and the atpI gene in mitogenome A. indica was transferred from a host plant like Miscanthus siensis. Cox2 (orf43) encodes proteins containing a membrane domain, making ORF (Open Reading Frame) the most likely candidate gene for CMS development in A. indica.

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“…This year saw a number of mitochondrial genomes published in short succession ( Guo et al. 2020 ; Kan et al. 2020 ; Sullivan et al.…”

Section: Introductionmentioning

confidence: 99%

Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure

Jackman

Coombe

Warren

et al. 2020

Genome Biology and Evolution

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Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

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The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

Cited by 59 publications

References 94 publications

Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS)

Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure

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