Complete Mitochondrial Genome Sequence of Sunflower (Helianthus annuus L.)

PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data

Complete mitochondrial genomes (mitogenomes) of plants are valuable resources for nucleocytoplasmic interactions, plant evolution, and plant cytoplasmic male sterile line breeding. However, the complete assembly of plant mitogenomes is challenging due to frequent recombination events and horizontal gene transfers. Previous studies have adopted Illumina, PacBio, and Nanopore sequencing data to assemble plant mitogenomes, but the poor assembly completeness, low sequencing accuracy, and high cost limit the sampling capacity. Here, we present an efficient assembly toolkit (PMAT) for de novo assembly of plant mitogenomes using low-coverage HiFi sequencing data. PMAT has been applied to the de novo assembly of 13 broadly representative plant mitogenomes, outperforming existing organelle genome assemblers in terms of assembly accuracy and completeness. By evaluating the assembly of plant mitogenomes from different sequencing data, it was confirmed that PMAT only requires 1× HiFi sequencing data to obtain a complete plant mitogenome. The source code for PMAT is available at https://github.com/bichangwei/PMAT. The developed PMAT toolkit will indeed accelerate the understanding of evolutionary variation and breeding application of plant mitogenomes.

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Diospyros oleifera, the first representative from the family Ebenaceae

Plant mitochondrial genomes are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitochondrial genome of any species in Ebenaceae has been reported. In this study, we reported the first mitochondrial genome of an Ebenaceae model plant Diospyros oleifera. The mitogenome was 493,958 bp in length, contained 39 protein-coding genes, 27 transfer RNA genes, and 3 ribosomal RNA genes. The rps2 and rps11 genes were missing in the D. oleifera mt genome, while the rps10 gene was identified. The length of the repetitive sequence in the D. oleifera mt genome was 31 kb, accounting for 6.33%. A clear bias in RNA-editing sites were found in the D. oleifera mt genome. We also detected 28 chloroplast-derived fragments significantly associated with D. oleifera mt genes, indicating intracellular tRNA genes transferred frequently from chloroplasts to mitochondria in D. oleifera. Phylogenetic analysis based on the mt genomes of D. oleifera and 27 other taxa reflected the exact evolutionary and taxonomic status of D. oleifera. Ka/Ks analysis revealed that 95.16% of the protein-coding genes in the D. oleifera mt genome had undergone negative selections. But, the rearrangement of mitochondrial genes has been widely occur among D. oleifera and these observed species. These results will lay the foundation for identifying further evolutionary relationships within Ebenaceae.

Identification of Medicinal Bidens Plants for Quality Control Based on Organelle Genomes

Bidens plants are annuals or perennials of Asteraceae and usually used as medicinal materials in China. They are difficult to identify by using traditional identification methods because they have similar morphologies and chemical components. Universal DNA barcodes also cannot identify Bidens species effectively. This situation seriously hinders the development of medicinal Bidens plants. Therefore, developing an accurate and effective method for identifying medicinal Bidens plants is urgently needed. The present study aims to use phylogenomic approaches based on organelle genomes to address the confusing relationships of medicinal Bidens plants. Illumina sequencing was used to sequence 12 chloroplast and eight mitochondrial genomes of five species and one variety of Bidens. The complete organelle genomes were assembled, annotated and analysed. Phylogenetic trees were constructed on the basis of the organelle genomes and highly variable regions. The organelle genomes of these Bidens species had a conserved gene content and codon usage. The 12 chloroplast genomes of the Bidens species were 150,489 bp to 151,635 bp in length. The lengths of the eight mitochondrial genomes varied from each other. Bioinformatics analysis revealed the presence of 50–71 simple sequence repeats and 46–181 long repeats in the organelle genomes. By combining the results of mVISTA and nucleotide diversity analyses, seven candidate highly variable regions in the chloroplast genomes were screened for species identification and relationship studies. Comparison with the complete mitochondrial genomes and common protein-coding genes shared by each organelle genome revealed that the complete chloroplast genomes had the highest discriminatory power for Bidens species and thus could be used as a super barcode to authenticate Bidens species accurately. In addition, the screened highly variable region trnS-GGA-rps4 could be also used as a potential specific barcode to identify Bidens species.

The Insights into Mitochondrial Genomes of Sunflowers

The significant difference in the mtDNA size and structure with simultaneous slow evolving genes makes the mitochondrial genome paradoxical among all three DNA carriers in the plant cell. Such features make mitochondrial genome investigations of particular interest. The genus Helianthus is a diverse taxonomic group, including at least two economically valuable species-common sunflower (H. annuus) and Jerusalem artichoke (H. tuberosus). The successful investigation of the sunflower nuclear genome provided insights into some genomics aspects and significantly intensified sunflower genetic studies. However, the investigations of organelles' genetic information in Helianthus, especially devoted to mitochondrial genomics, are presented by limited studies. Using NGS sequencing, we assembled the complete mitochondrial genomes for H. occidentalis (281,175 bp) and H. tuberosus (281,287 bp) in the current investigation. Besides the master circle chromosome, in the case of H. tuberosus, the 1361 bp circular plasmid was identified. The mitochondrial gene content was found to be identical for both sunflower species, counting 32 protein-coding genes, 3 rRNA, 23 tRNA genes, and 18 ORFs. The comparative analysis between perennial sunflowers revealed common and polymorphic SSR and SNPs. Comparison of perennial sunflowers with H. annuus allowed us to establish similar rearrangements in mitogenomes, which have possibly been inherited from a common ancestor after the divergence of annual and perennial sunflower species. It is notable that H. occidentalis and H. tuberosus mitogenomes are much more similar to H. strumosus than H. grosseserratus.

Organization Features of the Mitochondrial Genome of Sunflower (Helianthus annuus L.) with ANN2-Type Male-Sterile Cytoplasm

This study provides insights into the flexibility of the mitochondrial genome in sunflower (Helianthus annuus L.) as well as into the causes of ANN2-type cytoplasmic male sterility (CMS). De novo assembly of the mitochondrial genome of male-sterile HA89(ANN2) sunflower line was performed using high-throughput sequencing technologies. Analysis of CMS ANN2 mitochondrial DNA sequence revealed the following reorganization events: twelve rearrangements, seven insertions, and nine deletions. Comparisons of coding sequences from the male-sterile line with the male-fertile line identified a deletion of orf777 and seven new transcriptionally active open reading frames (ORFs): orf324, orf327, orf345, orf558, orf891, orf933, orf1197. Three of these ORFs represent chimeric genes involving atp6 (orf1197), cox2 (orf558), and nad6 (orf891). In addition, orf558, orf891, orf1197, as well as orf933, encode proteins containing membrane domain(s), making them the most likely candidate genes for CMS development in ANN2. Although the investigated CMS phenotype may be caused by simultaneous action of several candidate genes, we assume that orf1197 plays a major role in developing male sterility in ANN2. Comparative analysis of mitogenome organization in sunflower lines representing different CMS sources also allowed identification of reorganization hot spots in the mitochondrial genome of sunflower.

The alternative reality of plant mitochondrial DNA: One ring does not rule them all

Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across the broad community of life scientists that circular genome-sized molecules are the primary form of plant mitochondrial DNA, despite the understanding by plant mitochondrial researchers that this is an inaccurate and outdated concept. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative arrangements (isoforms). Most mitochondrial genomes have been assembled using methods unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. We characterized a comprehensive, complex set of isoforms within each species and compared genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms in our data, we infer that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other Lactuca species can be largely explained by rare recombination events that rearranged the structure. Our data demonstrate that representations of plant mitochondrial genomes as simple, circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)

Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression. Here, we used whole-chloroplast sequence data in combination with over 1000 nuclear single-nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to test alternative explanations for such discordance. Our phylogenetic analyses indicate that cytonuclear discordance is widespread within this group, both in terms of the relationships among species and among individuals within species. Simulations of chloroplast evolution show that incomplete lineage sorting cannot explain these patterns in most cases. Instead, most of the observed discordance is better explained by cytoplasmic introgression. Molecular tests of evolution further indicate that selection may have played a role in driving patterns of plastid variation - although additional experimental work is needed to fully evaluate the importance of selection on organellar variants in different parts of the geographic range. Overall, this study represents one of the most comprehensive tests of the drivers of cytonuclear discordance and highlights the potential for gene flow to lead to extensive organellar introgression in hybridizing taxa.

Assembly of the Mitochondrial Genome in the Campanulaceae Family Using Illumina Low-Coverage Sequencing

Platycodongrandiflorus (balloon flower) and Codonopsislanceolata (bonnet bellflower) are important herbs used in Asian traditional medicine, and both belong to the botanical family Campanulaceae. In this study, we designed and implemented a de novo DNA sequencing and assembly strategy to map the complete mitochondrial genomes of the first two members of the Campanulaceae using low-coverage Illumina DNA sequencing data. We produced a total of 28.9 Gb of paired-end sequencing data from the genomic DNA of P.grandiflorus (20.9 Gb) and C.lanceolata (8.0 Gb). The assembled mitochondrial genome of P.grandiflorus was found to consist of two circular chromosomes; the master circle contains 56 genes, and the minor circle contains 42 genes. The C.lanceolata mitochondrial genome consists of a single circle harboring 54 genes. Using a comparative genome structure and a pattern of repeated sequences, we show that the P.grandiflorus minor circle resulted from a recombination event involving the direct repeats of the master circle. Our dataset will be useful for comparative genomics and for evolutionary studies, and will facilitate further biological and phylogenetic characterization of species in the Campanulaceae.

The complete mitochondrial genome sequence of Chrysanthemum boreale (Asteraceae)

Chrysanthemum is an important ornamental, herbal, and medicinal plant. We report the complete mitochondrial genome (mitogenome) sequence of Chrysanthemum boreale. The mitogenome is 211,002 bp in length, has a GC content of 45.36%, and contains 58 genes, including 35 protein-coding genes, three ribosomal RNA genes, and 20 transfer RNA genes. A phylogenetic analysis based on mitogenome protein sequences from various plants confirmed that C. boreale belongs to the Asteraceae family. This mitogenome will be useful in evolutionary and phylogenetic studies of Chrysanthemum and Asteraceae.

Recombination Events Involving the atp9 Gene Are Associated with Male Sterility of CMS PET2 in Sunflower

Cytoplasmic male sterility (CMS) systems represent ideal mutants to study the role of mitochondria in pollen development. In sunflower, CMS PET2 also has the potential to become an alternative CMS source for commercial sunflower hybrid breeding. CMS PET2 originates from an interspecific cross of H. petiolaris and H. annuus as CMS PET1, but results in a different CMS mechanism. Southern analyses revealed differences for atp6, atp9 and cob between CMS PET2, CMS PET1 and the male-fertile line HA89. A second identical copy of atp6 was present on an additional CMS PET2-specific fragment. In addition, the atp9 gene was duplicated. However, this duplication was followed by an insertion of 271 bp of unknown origin in the 5' coding region of the atp9 gene in CMS PET2, which led to the creation of two unique open reading frames orf288 and orf231. The first 53 bp of orf288 are identical to the 5' end of atp9. Orf231 consists apart from the first 3 bp, being part of the 271-bp-insertion, of the last 228 bp of atp9. These CMS PET2-specific orfs are co-transcribed. All 11 editing sites of the atp9 gene present in orf231 are fully edited. The anther-specific reduction of the co-transcript in fertility-restored hybrids supports the involvement in male-sterility based on CMS PET2.

Sunflower Hybrid Breeding: From Markers to Genomic Selection

In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches combining omic technologies (genomics, transcriptomics, proteomics, metabolomics and phenomics) using bioinformatic tools will facilitate the identification of target genes and markers for complex traits and will give a better insight into the mechanisms behind the traits.