Multicentric origin and diversification of atp6‐orf79‐like structures reveal mitochondrial gene flows in Oryza rufipogon and Oryza sativa

He, Wenchuang; Chen, Caijin; Adedze, Yawo Mawunyo Nevame; Dong, Xilong; Xi, Kun; Sun, Yuena; Dang, Tengfei; Jiang, Deming

doi:10.1111/eva.13022

Cited by 20 publications

(15 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The read coverage depth of each contig was used to identify and remove the mis-assembled contigs derived from nuclear or mitochondrial genomes, which were usually lower than one-fifth the depth of plastid contigs. Other optimized options were also applied as reported in our previous study ( He et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

Chen

Xiang

et al. 2021

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.

show abstract

Section: Methodsmentioning

confidence: 99%

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

Chen

Xiang

et al. 2021

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The CMS-associated gene for BT-CMS is named orf79 because it encodes 79 amino acids (Akagi et al 1994;Iwabuchi et al 1993). Orf79 and its sequence variants, orfH79 and L-orf79, have been reported in HL-CMS (He et al 2020;Li et al 2008;Yi et al 2002) and LD-CMS (Itabashi et al 2009), respectively. The CDS of orfH79 and L-orf79 contain five and one nucleotide changes, respectively, compared with that of orf79 of BT-CMS, which lead to four and one amino acid substitutions, respectively.…”

Section: Mitochondrial Cms-associated Genesmentioning

confidence: 99%

“…ORFH79 of HL-CMS, which is encoded by a sequence variant of orf79, has been reported to interact with P61, a subunit of the cytochrome bc1 complex (mitochondrial electron transport chain complex III; Figure 4), resulting in energy production dysfunction and oxidative stress in mitochondria, which leads to abnormal pollen development (Wang et al 2013). The multicentric origin and diversification of atp6-orf79-like structures in O. rufipogon and O. sativa suggest that their divergence may have been beneficial to their survival during evolution (He et al 2020).…”

Section: Mitochondrial Cms-associated Genesmentioning

confidence: 99%

Molecular basis of cytoplasmic male sterility and fertility restoration in rice

Toriyama

2021

Plant Biotechnology

View full text Add to dashboard Cite

Cytoplasmic male sterility (CMS) is a maternally inherited trait that causes dysfunctions in pollen and anther development. CMS is caused by the interaction between nuclear and mitochondrial genomes. A product of a CMS-causing gene encoded by the mitochondrial genome affects mitochondrial function and the regulation of nuclear genes, leading to male sterility. In contrast, the RESTORER OF FERTILITY gene (Rf gene) in the nuclear genome suppresses the expression of the CMS-causing gene and restores male fertility. An alloplasmic CMS line is often bred as a result of nuclear substitution, which causes the removal of functional RF genes and allows the expression of a CMS-causing gene in mitochondria. The CMS/Rf system is an excellent model for understanding the genetic interactions and cooperative functions of mitochondrial and nuclear genomes in plants, and is also an agronomically important trait for hybrid seed production. In this review article, pollen and anther phenotypes of CMS, CMS-associated mitochondrial genes, Rf genes, and the mechanism that causes pollen abortion and its agronomical application for rice are described.

show abstract

“…The variability of plant mitochondrial genomes can even fluctuate greatly within a species [ 11 , 12 ]. Structural rearrangements in mitochondrial genes can have important outcomes for survival as in the case of gene chimerism resulting in cytoplasmic male sterility [ 13 ]. Another important feature of plant mitochondrial genome evolution is gene or sequence transfer to the nuclear and chloroplast genomes [ 8 , 14 – 16 ].…”

Section: Introductionmentioning

confidence: 99%

A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

Hong

Liao

et al. 2021

BMC Genomics

View full text Add to dashboard Cite

Background Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. Results We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. Conclusion For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.

show abstract

Multicentric origin and diversification of atp6‐orf79‐like structures reveal mitochondrial gene flows in Oryza rufipogon and Oryza sativa

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 20 publications

References 77 publications

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

Molecular basis of cytoplasmic male sterility and fertility restoration in rice

A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

Contact Info

Product

Resources

About