De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination

Yang, Zhijian; Ni, Yang; Lin, Zhien; Yang, Liubin; Chen, Guotai; Nijiati, Nuerla; Hu, Yunzhuo; Chen, Xuanyang

doi:10.1186/s12870-022-03665-y

Cited by 37 publications

(39 citation statements)

References 61 publications

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“…As an increasing number of mitogenomes are published, studies have found that the size of plant mitogenomes varies greatly, ranging from 66 kb to 11.7 Mb [ 12 , 27 ]. Additionally, studies have revealed that plant mitogenomes differ from chloroplast genomes (always containing the conserved single loop structure) and should be presented in multiple sequence units to show the dynamic connection of the mitogenome [ 3 , 5 , 6 , 28 , 29 ]. The complete mitochondrial genome of Th.…”

Section: Discussionmentioning

confidence: 99%

“…SSRs and dispersed repeats are important components of repeat sequences in the mitochondrial genome [ 5 , 6 , 8 ]. By comparing the repeat sequences of 7 gymnosperm mitogenomes, it is interesting to find that the number of SSRs in gymnosperms form a definite hierarchy and could well reflect the phylogenetic relationship.…”

Section: Discussionmentioning

confidence: 99%

“…Due to the complicated physical structure, sequence composition, and abundance of repeat sequences, there are still certain challenges associated with the assembly and annotation of vascular plant mitochondrial genomes [ 1 – 5 ]. An increasing number of plant mitochondrial genomes are being reported as a result of the ongoing advancements in sequencing technology [ 5 – 8 ]. However, gymnosperms only make up a small portion of the published plant mitogenomes; the majority come from angiosperms.…”

Section: Introductionmentioning

confidence: 99%

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Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

Xia

Zuo

et al. 2023

BMC Plant Biol

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Background The complex physical structure and abundant repeat sequences make it difficult to assemble the mitogenomes of seed plants, especially gymnosperms. Only approximately 33 mitogenomes of gymnosperms have been reported. However, as the most widely distributed and the second largest family among gymnosperms, Cupressaceae has only six assembled mitogenomes, including five draft mitogenomes and one complete mitogenome, which has greatly hindered the understanding of mitogenome evolution within this large family, even gymnosperms. Results In this study, we assembled and validated the complete mitogenome of Thuja sutchuenensis, with a size of 2.4 Mb. Multiple sequence units constituted its complex structure, which can be reduced to three linear contigs and one small circular contig. The analysis of repeat sequences indicated that the numbers of simple sequence repeats increased during the evolutionary history of gymnosperms, and the mitogenome of Thuja sutchuenensis harboured abundant extra-long repeats (more than 5 kb). Additionally, the longest repeat sequence identified in these seven gymnosperms also came from the mitogenome of Thuja sutchuenensis, with a length of up to 47 kb. The analysis of colinear blocks and gene clusters both revealed that the orders of mitochondrial genes within gymnosperms was not conserved. The comparative analysis showed that only four tRNAs were shared by seven gymnosperms, namely, trnD-GUC, trnE-UUC, trnI-CAU and trnY-GUA. Furthermore, four genes have undergone potential positive selection in most gymnosperm species, namely, atp8, ccmB, mttB and sdh4. Conclusion We successfully assembled the second complete mitogenome within Cupressaceae and verified that it consisted of multiple sequence units. Our study also indicated that abundant long repeats may contribute to the generation of the complex conformation of the mitogenome of Thuja sutchuenensis. The investigation of Thuja sutchuenensis’s mitogenome in our study provides new insight into further understanding the complex mitogenome architecture within gymnosperms.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

Xia

Zuo

et al. 2023

BMC Plant Biol

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“…For example, the mitogenome of Populus simonii was assembled into three circular molecules, and all of them had protein-coding capability ( Bi et al., 2022 ). Additionally, the sweet potato ( Ipomoea batatas [L.] Lam) mitogenome was found to have a multicircular structure generated by repeat sequence-mediated recombination ( Yang et al., 2022 ). The mitogenome of plants is much larger than that of other eukaryotes and differs even among related species ( Kubo and Newton, 2008 ; Sloan et al., 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Assembly and comparative analysis of the complete mitochondrial genome of Salix wilsonii using PacBio HiFi sequencing

Han

Chen

et al. 2022

Front. Plant Sci.

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Salix L. (willows) is one of the most taxonomically complex genera of flowering plants, including shrubs, tall trees, bushes, and prostrate plants. Despite the high species diversity, only five mitochondrial genomes (mitogenomes) have been released in this genus. Salix wilsonii is an important ornamental and economic willow tree in section Wilsonia of the genus Salix. In this study, the S. wilsonii mitogenome was assembled into a typical circular structure with a size of 711,456 bp using PacBio HiFi sequencing. A total of 58 genes were annotated in the S. wilsonii mitogenome, including 33 protein-coding genes (PCGs), 22 tRNAs, and 3 rRNAs. In the S. wilsonii mitogenome, four genes (mttB, nad3, nad4, and sdh4) were found to play important roles in its evolution through selection pressure analysis. Collinearity analysis of six Salix mitogenomes revealed high structural variability. To determine the evolutionary position of S. wilsonii, we conducted a phylogenetic analysis of the mitogenomes of S. wilsonii and 12 other species in the order Malpighiales. Results strongly supported the segregation of S. wilsonii and other five Salix species with 100% bootstrap support. The comparative analysis of the S. wilsonii mitogenome not only sheds light on the functional and structural features of S. wilsonii but also provides essential information for genetic studies of the genus Salix.

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“…Differences in mitogenome size can be attributed to repetitive sequences and foreign DNA derived from other organisms during evolution [ 9 ]. Many intramolecular recombination events and subgenomic conformations have been found in some land plants, such as Scutellaria tsinyunensis [ 10 ], Cucumis sativus [ 11 ], Ipomoea batatas [ 12 ], and Brassica napus [ 13 ]. In extreme environments, gene loss and RNA edits may occur during plant mitogenome rearrangement [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants

Yang

Ling

Zhang

et al. 2022

Genes

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Actinidiaceae, an economically important plant family, includes the Actinidia, Clematoclethra and Saurauia genus. Kiwifruit, with remarkably high vitamin C content, is an endemic species widely distributed in China with high economic value. Although many Actinidiaceae chloroplast genomes have been reported, few complete mitogenomes of Actinidiaceae have been studied. Here, complete circular mitogenomes of the four kiwifruit species and Saurauia tristyla were assembled. Codon usage, sequence repeats, RNA editing, gene transfers, selective pressure, and phylogenetic relationships in the four kiwifruit species and S. tristyla were comparatively analyzed. This research will contribute to the study of phylogenetic relationships within Actiniaceae and molecular barcoding in kiwifruit.

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De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination

Cited by 37 publications

References 61 publications

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

Assembly and comparative analysis of the complete mitochondrial genome of Salix wilsonii using PacBio HiFi sequencing

A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants

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