The Insights into Mitochondrial Genomes of Sunflowers

The first mitochondrial genome of Calophyllum soulattri Burm.f

Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( ≥ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri's evolution and Malpighiales' phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.

The complete mitochondrial genome of Cuminum cyminum (Apiales: Apiaceae) and phylogenetic analysis

Cumin (Cuminum cyminum L). belongs to the family Apiaceae and the order Apiales, which is a widely grown spice and medicinal plant in Xinjiang province, China. In the current study, whole genome sequencing of C. cyminum was performed using the Illumina HiSeq 4000 platform, and the complete mitogenome sequence was assembled and annotated. We found that the single circular mitogenome of C. cyminum was 246,721 bp in length, and has about 45.5% GC content. It comprised 73 genes in the coding region (35 protein-coding genes, 18 tRNA genes, 3 rRNA genes, and 15 open-reading frames) and a non-coding region. Phylogenetic analysis indicated that C. cyminum is closely related to Daucus carota and the subtribes Daucinae. The mitogenome of C. cyminum revealed its phylogenetic relationships with other species in the Apiaceae family, which would further help in understanding its evolution.

Mitogenomic Research of Silverleaf Sunflower (Helianthus argophyllus) and Its Interspecific Hybrids

Interspecific hybridization is widespread for sunflowers, both in wild populations and commercial breeding. One of the most common species that can efficiently cross with Helianthus annuus is the Silverleaf sunflower-Helianthus argophyllus. The current study carried out structural and functional organization analyses of mitochondrial DNA in H. argophyllus and the interspecific hybrid, H. annuus (VIR114A line) × H. argophyllus. The complete mitogenome of H. argophyllus counts 300,843 bp, has a similar organization to the mitogenome of cultivated sunflower, and holds SNPs typical for wild sunflowers. RNA editing analysis predicted 484 sites in H. argophyllus mitochondrial CDS. The mitochondrial genome of the H. annuus × H. argophyllus hybrid is identical to the maternal line (VIR114A). We expected that significant rearrangements in the mitochondrial DNA of the hybrid would occur, due to the frequent recombination. However, the hybrid mitogenome lacks rearrangements, presumably due to the preservation of nuclear-cytoplasmic interaction paths.

NGS Reads Dataset of Sunflower Interspecific Hybrids

The sunflower (Helianthus annuus), which belongs to the family of Asteraceae, is a crop grown worldwide for consumption by humans and livestock. Interspecific hybridization is widespread for sunflowers both in wild populations and commercial breeding. The current dataset comprises 250 bp and 76 paired-end NGS reads for six interspecific sunflower hybrids (F1). The dataset aimed to expand Helianthus species genomic information and benefit genetic research, and is useful in alloploids’ features investigations and nuclear–organelle interactions studies. Mitochondrial genomes of perennial sunflower hybrids H. annuus × H. strumosus and H. annuus × H. occidentalis were assembled and compared with parental forms.

Sequencing and analysis of the complete mitochondrial genomes of Toona sinensis and Toona ciliata reveal evolutionary features of Toona

BACKGROUND

Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives.

RESULTS

(1) T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other.

CONCLUSIONS

This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.

Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales

BACKGROUND

Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales.

RESULTS

Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall.

CONCLUSIONS

The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.

Characterization and Phylogenetic Analyses of the Complete Mitochondrial Genome of Sugarcane (Saccharum spp. Hybrids) Line A1

Modern sugarcane cultivars are highly polyploid with complex nuclear genomic genetic background, while their mitochondrion (mt) genomes are much simpler, smaller and more manageable and could provide useful phylogenetic information. In this study, the mt genome of a modern commercial cultivar A1 was sequenced via Illumina Hiseq XTen and PacBio Sequel platform. The assembled and annotated mitochondrial genomes of A1 were composed of two circular DNA molecules, one large and one small, which were named Chromosome 1 and Chromosome 2. The two distinct circular chromosomes of mitogenome construct is consisted with other sugarcane cultivars i.e., Saccharum officinarum Khon Kaen 3 and Saccharum spp. hybrids ROC22 and FN15. The Chromosome 1 of A1 mitogenome is 300,822 bp in length with the GC content of 43.94%, and 7.14% of Chromosome 1 sequences (21,468 nucleotides) are protein coding genes (PCGs) while 92.86% (279,354 nucleotides) are intergenic region. The length of Chromosome 2 is 144,744 bp with the GC content of 43.57%, and 8.20% of Chromosome 2 sequences (11,865 nucleotides) are PCGs while 91.80% (132,879 nucleotides) are intergenic region. A total of 43 genes are located on Chromosome 1, which contains 22 PCGs (six nad genes, four rps genes, four atp genes, three ccm genes, three cox genes, one mat gene and one mtt gene) and 21 non-coding genes including 15 tRNAs and 6 rRNAs. Chromosome 2 includes 18 genes in total, which contains 13 PCGs (four nad genes, three rps genes, two atp genes, one ccm gene, one cob gene, one cox gene and one rpl gene) and five non-coding genes (tRNA genes). Analysis of codon usage of 35 PCGs showed that codon ending in A/U was preferred. Investigation of gene composition indicated that the types and copy numbers of CDS genes, tRNAs and rRNAs of A1 and FN15 were identical. The cox1 gene has two copies and the trnP gene has one copy in A1, FN15 and ROC22 three lines, while there is only one copy of cox1 and two copies of trnP in S. officinarum Khon Kaen 3. In addition, S. officinarum Khon Kaen 3 have no nad1 gene and rps7 gene. 100 sequence repeats, 38 SSRs and 444 RNA editing sites in A1 mt genome were detected. Moreover, the maximum likelihood phylogenetic analysis found that A1 were more closely related to S. spp. hybrid (ROC22 and FN15) and S. officinarum (Khon Kaen 3). Herein, the complete mt genome of A1 will provide essential DNA molecular information for further phylogenetic and evolutionary analysis for Saccharum and Poaceae.