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

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.

Induce male sterility by CRISPR/Cas9-mediated mitochondrial genome editing in tobacco

Genome editing has become more and more popular in animal and plant systems following the emergence of CRISPR/Cas9 technology. However, target sequence modification by CRISPR/Cas9 has not been reported in the plant mitochondrial genome, mtDNA. In plants, a type of male sterility known as cytoplasmic male sterility (CMS) has been associated with certain mitochondrial genes, but few genes have been confirmed by direct mitochondrial gene-targeted modifications. Here, the CMS-associated gene (mtatp9) in tobacco was cleaved using mitoCRISPR/Cas9 with a mitochondrial localization signal. The male-sterile mutant, with aborted stamens, exhibited only 70% of the mtDNA copy number of the wild type and exhibited an altered percentage of heteroplasmic mtatp9 alleles; otherwise, the seed setting rate of the mutant flowers was zero. Transcriptomic analyses showed that glycolysis, tricarboxylic acid cycle metabolism and the oxidative phosphorylation pathway, which are all related to aerobic respiration, were inhibited in stamens of the male-sterile gene-edited mutant. In addition, overexpression of the synonymous mutations dsmtatp9 could restore fertility to the male-sterile mutant. Our results strongly suggest that mutation of mtatp9 causes CMS and that mitoCRISPR/Cas9 can be used to modify the mitochondrial genome of plants.

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.