Comparative analysis of mitochondrial genomes of soybean cytoplasmic male-sterile lines and their maintainer lines

Genomic variation and evolutionary patterns in organelle genomes between annual and perennial Glycine species

BACKGROUND

The complexity of structural variations and long stretches of repetitive DNA make the analysis of plant mitochondrial genomes (mitogenomes) exceptionally challenging. A thorough investigation of plant mitogenomes is essential for uncovering the evolutionary processes of plant organelles and optimizing traits related to plant cellular metabolism. The genus Glycine includes groups with both perennial and annual life strategies, making it an ideal subject for studying the complexity and variations of plant mitogenomes during evolution across different life strategies.

RESULTS

Here, we assembled 20 complete mitochondrial and plastid genomes of Glycine accessions, including both annual and perennial species using the latest organelle genome assembly tool. Significant structural variations and differences in tRNA content were observed in the mitogenomes between the two life-history strategy subgenera, while protein-coding genes and rRNAs content were highly conserved. Distinct patterns of nuclear plastid DNAs and nuclear mitochondrial DNAs (NUPTs/NUMTs) were uncovered among annual and perennial species. Genes residing in NUMTs (NUMGs) showed a substantial presence in Glycine accessions, with annual soybeans exhibiting a higher proportion of protein-coding genes fully integrated into the nuclear genome. Phylogenetic analysis indicated a closely related evolutionary trajectory between mitochondrial and nuclear genomes in Glycine, providing supplementary evidence relevant to the evolutionary history of Glycine.

CONCLUSIONS

This study showed the structural variations and evolutionary patterns of mitochondrial genomes between annual and perennial Glycine species. These findings contribute to our understanding of plant organelle complexity, variation and history of intracellular genomic integration.

De novo assembly and characterization of the complete mitochondrial genome of Phellodendron amurense reveals three repeat-mediated recombination

Phellodendron amurense Rupr., a rare herb renowned for its medicinal and ecological significance, has remained genetically unexplored at the mitochondrial level until now. This study presents the first-ever systematic assembly and annotation of the complete mitochondrial genome of P. amurense, achieved through a hybrid strategy combining Illumina and Nanopore sequencing data. The mitochondrial genome spans 566,285 bp with a GC content of 45.51 %, structured into two circular molecules. Our comprehensive analysis identified 32 protein-coding genes (PCGs), 33 tRNA genes, and 3 rRNA genes, alongside 181 simple sequence repeats, 19 tandem repeats, and 310 dispersed repeats. Notably, multiple genome conformations were predicted due to repeat-mediated homologous recombination. Additionally, we assembled the chloroplast genome, identifying 21 mitochondrial plastid sequences that provide insights into organelle genome interactions. A total of 380 RNA-editing sites within the mitochondrial PCGs were predicted, enhancing our understanding of gene regulation and function. Phylogenetic analysis using mitochondrial PCGs from 30 species revealed evolutionary relationships, confirming the homology between P. amurense and Citrus species. This foundational study offers a valuable genetic resource for the Rutaceae family, facilitating further research into genetic evolution and molecular diversity in plant mitochondrial genomes.

Past and future of cytoplasmic male sterility and heterosis breeding in crop plants

Plant breeding needs to embrace genetic innovations to ensure stability in crop yields under fluctuating climatic conditions. Development of commercial hybrid varieties has proven to be a sustainable and economical alternative to deliver superior yield, quality and resistance with uniformity in a number of food crops. Cytoplasmic male sterility (CMS), a maternally inherited inability to produce functional pollen, facilitates a three-line system for efficient hybrid seed production strategies in crops. The CMS system has illustrated its potential as a robust pollination control mechanism to support the billion-dollar seed industry. In plants, CMS arises due to a genomic conflict between mitochondrial open reading frames (orfs) and nuclear-encoding restoration-of-fertility (Rf) genes, leading to floral abnormalities and pollen sterility. Research on pollen sterility and fertility restoration provides deeper insights into cytoplasmic-nuclear interplay in plants and elucidates key molecular targets for hybrid breeding in crops. More recently, programmable gene editing (e.g., TALEN, CRISPR-Cas) has emerged as a promising tool to functionally validate CMS and Rf genes and obviate the need for pollen donors or Rf-genes for hybrid breeding. Modern genomic prediction models have allowed establishment of high-performing heterotic groups and patterns for sustaining long-term gain in hybrid breeding. This article reviews latest discoveries elucidating the molecular mechanisms behind CMS and fertility restoration in plants. We then present our perspective on how evolving genetic technologies are contributing to advance fundamental knowledge of the CMS-Rf genetic system for producing crop hybrids with high heterosis.

Comparative analysis of mitochondrial genomes of Stemona tuberosa lour. reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

BACKGROUND

Stemona tuberosa, a vital species in traditional Chinese medicine, has been extensively cultivated and utilized within its natural distribution over the past decades. While the chloroplast genome of S. tuberosa has been characterized, its mitochondrial genome (mitogenome) remains unexplored.

RESULTS

This paper details the assembly of the complete S. tuberosa mitogenome, achieved through the integration of Illumina and Nanopore sequencing technologies. The assembled mitogenome is 605,873 bp in size with a GC content of 45.63%. It comprises 66 genes, including 38 protein-coding genes, 25 tRNA genes, and 3 rRNA genes. Our analysis delved into codon usage, sequence repeats, and RNA editing within the mitogenome. Additionally, we conducted a phylogenetic analysis involving S. tuberosa and 17 other taxa to clarify its evolutionary and taxonomic status. This study provides a crucial genetic resource for evolutionary research within the genus Stemona and other related genera in the Stemonaceae family.

CONCLUSION

Our study provides the inaugural comprehensive analysis of the mitochondrial genome of S. tuberosa, revealing its unique multi-branched structure. Through our investigation of codon usage, sequence repeats, and RNA editing within the mitogenome, coupled with a phylogenetic analysis involving S. tuberosa and 17 other taxa, we have elucidated its evolutionary and taxonomic status. These investigations provide a crucial genetic resource for evolutionary research within the genus Stemona and other related genera in the Stemonaceae family.

Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant

BACKGROUND

Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported.

RESULTS

In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted.

CONCLUSIONS

This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.

Mitochondrial genome features and systematic evolution of diospyros kaki thunb 'Taishuu'

BACKGROUND

'Taishuu' has a crisp texture, abundant juice, and sweet flavor with hints of cantaloupe. The availability of mitochondrial genome data of Diospyros species is far from the known number of species.

RESULTS

The sequencing data were assembled into a closed circular mitochondrial chromosome with a 421,308 bp length and a 45.79% GC content. The mitochondrial genome comprised 40 protein-coding, 24 tRNA, and three rRNA genes. The most common codons for arginine (Arg), proline (Pro), glycine (Gly), tryptophan (Trp), valine (Val), alanine (Ala), and leucine (Leu) were AGA, CCA, GGA, UGG, GUA, GCA, and CUA, respectively. The start codon for cox1 and nad4L protein-coding genes was ACG (ATG), whereas the remaining protein-coding genes started with ATG. There are four types of stop codons: CGA, TAA, TAG, and TGA, with TAA being the most frequently used stop codon (45.24%). In the D. kaki Thunb. 'Taishuu' mitochondrial genome, a total of 645 repeat sequences were identified, including 125 SSRs, 7 tandem repeats, and 513 dispersed repeats. Collinearity analysis revealed a close relationship between D. kaki Thunb. 'Taishuu' and Diospyros oleifera, with conserved homologous gene fragments shared among these species in large regions of the mitochondrial genome. The protein-coding genes ccmB and nad4L were observed to undergo positive selection. Analysis of homologous sequences between chloroplasts and mitochondria identified 28 homologous segments, with a total length of 24,075 bp, accounting for 5.71% of the mitochondrial genome. These homologous segments contain 8 annotated genes, including 6 tRNA genes and 2 protein-coding genes (rrn18 and ccmC). There are 23 homologous genes between chloroplasts and nuclei. Mitochondria, chloroplasts, and nuclei share two homologous genes, which are trnV-GAC and trnW-CCA.

CONCLUSION

In conclusion, a high-quality chromosome-level draft genome for D. kaki was generated in this study, which will contribute to further studies of major economic traits in the genus Diospyros.

Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion

Cytoplasmic male sterility (CMS) has been widely exploited for hybrid seed production in onions (Allium cepa L.). In contrast to long-day onion cultivars, short-day onion has not yet been investigated for mitochondrial genome structure and DNA rearrangements associated with CMS activity. Here, we report the 3,16,321 bp complete circular mitochondrial genome of tropical onion CMS line (97A). Due to the substantial number of repetitive regions, the assembled mitochondrial genome of maintainer line (97B) remained linear with 15 scaffolds. Additionally, 13 and 20 chloroplast-derived fragments with a size ranging from 143 to 13,984 bp and 153-17,725 bp were identified in the 97A and 97B genomes, respectively. Genome annotation revealed 24 core protein-coding genes along with 24 and 28 tRNA genes in the mitochondrial genomes of 97A and 97B, respectively. Furthermore, comparative genome analysis of the 97A and 97B mitochondrial genomes showed that gene content was almost similar except for the chimeric ORF725 gene which is the extended form of the COX1 gene.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03850-2.

The complete plastid genome and characteristics analysis of Achillea millefolium

Achillea is a crop with Chinese herbal characteristics and horticultural values. Its leaves and flowers contain aromatic oil, and the ripe herb can also be used as medicine to induce sweat and relieve rheumatic pains. It is seen cultivated in gardens all over China. Currently, the most comprehensive chloroplast genome sample involved in the study refers to New World clades of Achillea, which are used for marker selection and phylogenetic research. We completely sequenced the chloroplast genomes of Achillea millefolium. These sequencing results showed that the plastid genome is 149,078 bp in size and possesses a typical quadripartite structure containing one large single copy (LSC) with 82,352 bp, one small single copy (SSC) with 18,426 bp, and a pair of inverted repeat (IR) regions with 24,150 bp in Achillea millefolium. The chloroplast genome encodes a common number of genes, of which 88 are protein-coding genes, 37 transfer ribonucleic acid genes, and 8 ribosomal ribonucleic acid genes, which are highly similar in overall size, genome structure, gene content, and sequence. The exact similarity was observed when compared to other Asteraceae species. However, there were structural differences due to the restriction or extension of the inverted repeat (IR) regions-the palindromic repeats being the most prevalent form. Based on 12 whole-plastomes, 3 hypervariable regions (rpoB, rbcL, and petL-trnP-UGG) were discovered, which could be used as potential molecular markers.

When does the female bias arise? Insights from the sex determination cascade of a flea beetle with a strongly skewed sex ratio

Reproduction-manipulating bacteria like Wolbachia can shift sex ratios in insects towards females, but skewed sex ratios may also arise from genetic conflicts. The flea beetle Altica lythri harbors three main mtDNA strains that are coupled to three different Wolbachia infections. Depending on the mtDNA types, the females produce either offspring with a balanced sex ratio or exclusively daughters. To obtain markers that can monitor when sex bias arises in the beetle's ontogeny, we elucidated the sex determination cascade of A. lythri. We established a RT-PCR method based on length variants of dsx (doublesex) transcripts to determine the sex of morphologically indistinguishable eggs and larvae. In females of one mtDNA type (HT1/HT1*) known to produce only daughters, male offspring were already missing at the egg stage while for females of another type (HT2), the dsx splice variants revealed a balanced sex ratio among eggs and larvae. Our data suggest that the sex determination cascade in A. lythri is initiated by maternally transmitted female-specific tra (transformer) mRNA as primary signal. This tra mRNA seems to be involved in a positive feedback loop that maintains the production of the female splice variant, as known for female offspring in Tribolium castaneum. The translation of the maternally transmitted female tra mRNA must be inhibited in male offspring, but the underlying primary genetic signal remains to be identified. We discuss which differences between the mtDNA types can influence sex determination and lead to the skewed sex ratio of HT1.

Polymorphism analysis of the chloroplast and mitochondrial genomes in soybean

BACKGROUND

Soybean is an important protein- and oil-rich crop throughout the world. Much attention has been paid to its nuclear genome, which is bi-parentally inherited and associated with many important agronomical traits. However, less is known about the genomes of the semi-autonomous and essential organelles, chloroplasts and mitochondria, of soybean.

RESULTS

Here, through analyzing the polymorphisms of these organelles in 2580 soybean accessions including 107 wild soybeans, we found that the chloroplast genome is more variable than the mitochondrial genome in terms of variant density. Consistent with this, more haplotypes were found in the chloroplast genome (44 haplotypes) than the mitochondrial genome (30 haplotypes). These haplotypes were distributed extremely unevenly with the top two haplotypes (CT1 and CT2 for chloroplasts, MT1 and MT2 for mitochondria) accounting for nearly 70 and 18% of cultivated soybean accessions. Wild soybeans also exhibited more diversity in organelle genomes, harboring 32 chloroplast haplotypes and 19 mitochondrial haplotypes. However, only a small percentage of cultivated soybeans shared cytoplasm with wild soybeans. In particular, the two most frequent types of cytoplasm (CT1/MT1, CT2/MT2) were missing in wild soybeans, indicating that wild soybean cytoplasm has been poorly exploited during breeding. Consistent with the hypothesis that soybean originated in China, we found that China harbors the highest cytoplasmic diversity in the world. The geographical distributions of CT1-CT3 and MT1-MT3 in Northeast China were not significantly different from those in Middle and South China. Two mitochondrial polymorphism sites, p.457333 (T > C) and p.457550 (G > A), were found to be heterozygous in most soybeans, and heterozygosity appeared to be associated with the domestication of cultivated soybeans from wild soybeans, the improvement of landraces to generate elite cultivated soybeans, and the geographic adaptation of soybean.

CONCLUSIONS

The haplotypes of thousands of soybean cultivars should be helpful in evaluating the impact of cytoplasm on soybean performance and in breeding cultivars with the desired cytoplasm. Mitochondrial heterozygosity might be related to soybean adaptation, and this hypothesis needs to be further investigated.

Comparison of Mitochondrial Genomes between a Cytoplasmic Male-Sterile Line and Its Restorer Line for Identifying Candidate CMS Genes in Gossypium hirsutum

As the core of heterosis utilization, cytoplasmic male sterility (CMS) has been widely used in hybrid seed production. Previous studies have shown that CMS is always closely related to the altered programming of mitochondrial genes. To explore candidate CMS genes in cotton (Gossypium hirsutum), sequencing and de novo assembly were performed on the mitochondrial genome of the G. hirsutum CMS line SI3A, with G. harknessii CMS-D2 cytoplasm, and the corresponding G. hirsutum restorer line 0-613-2R. Remarkable variations in genome structure and gene transcripts were detected. The mitochondrial genome of SI3A has three circle molecules, including one main circle and two sub-circles, while 0-613-2R only has one. RNA-seq and RT-qPCR analysis proved that orf606a and orf109a, which have a chimeric structure and transmembrane domain, were highly expressed in abortive anthers of SI3A. In addition, comparative analysis of RNA-seq and full-length transcripts revealed the complex I gene nad4 to be expressed at a lower level in SI3A than in its restorer and that it featured an intron retention splicing pattern. These two novel chimeric ORFs and nad4 are potential candidates that confer CMS character in SI3A. This study provides new insight into the molecular basis of the nuclear–cytoplasmic interaction mechanism, and that putative CMS genes might be important sources for future precise design cross-breeding of cotton.

Comparative analysis of mitochondrial genomes provides insights into the mechanisms underlying an S-type cytoplasmic male sterility (CMS) system in wheat (Triticum aestivum L.)

Cytoplasmic male sterility (CMS) has been widely used in crop cross breeding. There has been much research on wheat CMS. However, the correlation between S-type CMS and mitochondrial genome remains elusive. Herein, we sequenced the mitochondrial genome of wheat CMS line and compared it with the maintainer line. The results showed that the mitochondrial genome of CMS line encoded 26 tRNAs, 8 rRNAs, and 35 protein-coding genes, and the cob encoding complex III in which the protein coding gene is mutated. This protein is known to affect reactive oxygen (ROS) production. The analysis of ROS metabolism in developing anthers showed that the deficiency of antioxidants and antioxidant enzymes in the sterile system aggravated membrane lipid oxidation, resulting in ROS accumulation, and influencing the anther development. Herein, cob is considered as a candidate causative gene sequence for CMS.