Maternal inheritance of mitochondrial genomes and complex inheritance of chloroplast genomes in Actinidia Lind.: evidences from interspecific crosses

Phylogenomic conflict analyses of plastid and mitochondrial genomes of Impatiens (Balsaminaceae) reveal its complex evolutionary history

Impatiens is among the most diverse angiosperm genera, comprising more than 1000 species. The phylogenetic relationship among sections of Impatiens remains unclear. Plastomes and mitogenomes are useful for resolving problematic relationships in plant phylogenetics; however, conflicts between the organellar genomes have been reported. Here, we reconstructed the phylogeny of Impatiens using concatenated and multispecies coalescent (MSC) methods based on coding and noncoding regions of the plastome and coding regions of the mitogenome from 139 species, representing all major clades in Impatiens. Conflict analyses were conducted to test and visualize the incongruences between the organellar genomes and within the plastome. The analyses supported the monophyly of all subgenera and sections and identified a new clade (clade Longlinensis), but the relationships among these sections are inconsistent. There was incongruence between the organellar genome trees regarding the relationships among sect. Semeiocardium, sect. Racemosae and clade Longlinensis. There was also incongruence within the plastome regarding the relationships among sections Fasciculatae, Impatiens, Tuberosae, Scorpioidae, and Uniflorae. Our results show that incongruence between organellar genomes likely results from the complex evolutionary history of the genus, involving mixed inheritance of organellar genomes and hybridization. The incongruence within the plastome may result from the limited phylogenetic signal in plastome data, which could be due to the rapid radiation between 15.07 and 12.93 Ma. Specific genes and regions that led to such incongruence have been identified. By confirming the monophyly of Impatiens sections and detecting phylogenetic conflicts, this study provides a unique plastid and mitogenomic perspective on Impatiens phylogeny.

Comparative chloroplast genomics provides insights into the phylogenetic relationships and evolutionary history for Actinidia species

Actinidia species are fruit trees with various functions, such as providing edible fruit, serving as ornamental plants, and having medicinal benefits. However, the taxonomy of Actinidia species is controversial due to widespread hybridization, the history of divergence and polyploid speciation among Actinidia species also remains unclear. In this study, we conducted comparative analyses of the chloroplast genomes and ploidy among multiple Actinidia species. The genes clpP, infA, ndhD, ndhK, and rpl20 were absent from these chloroplast genomes. The ycf2 and rpl20 genes in the Actinidia species were under positive selection. Several regions (rps16-trnQ-UUG, trnS-GCU-trnR-UCU, ndhC-trnV-UAC, rbcL-accD, rps12-psbB, trnN-GUU-ndhF, ycf1-trnN-GUU, and trnH-GUG-psbA) and genes (ycf1, ycf2, accD, rpl20) exhibited high variability, which could potentially serve as molecular markers in species delineation and other phylogenetic studies. Through divergence time estimation, the Actinidia genus originated 23 million years ago (Ma), and experienced a tetraploidization event in ~ 20 Ma. Subsequently, Actinidia has undergone extensive diploidization. Our findings will provide valuable information in species identification, breeding programs, and conservation efforts for Actinidia species.

Endosperm culture-based allotriploid hybrid production from an interspecific cross of Haemanthus spp.: new insights into polyploidization and hybridization

BACKGROUND

Allopolyploid plants are valuable for plant breeding because they have the advantage of polyploidization and hybridization, such as increased vigor and adaptability. Although biparental triploid endosperms have the potential to be used to produce allotriploid plants, the approach remains largely unexplored. Therefore, this study aimed to produce allotriploid plants from the endosperms of interspecific crosses between Haemanthus pauculifolius and H. albiflos.

RESULTS

Precisely identified embryo and endosperm pairs were used. Embryos were grown on half-strength Murashige and Skoog (MS) medium, and endosperms from interspecific crossing were cultured to induce callus formation and shoot regeneration, which then developed into plantlets. MS medium supplemented with 4-amino-3,5,6-trichloropicolinic acid (picloram) and 6-benzylaminopurine (BAP), or 2,4-dichloro phenoxy acetic acid (2,4-D) and BAP were used for callus induction, and callus formation rates were measured. Flow cytometry, karyotyping, and Sanger sequencing of the nuclear internal transcribed spacer (ITS) region, chloroplast (trnL-trnF region, matK gene), and mitochondrial (nad1 gene) DNA were performed on plantlets derived from embryos and endosperms, along with their parental plants. In this study, a total of 18 pairs of diploid and triploid plantlets were obtained from the embryo and endosperm, respectively. Callus formation rates were significantly higher on media with picloram and BAP compared to 2,4-D and BAP. ITS sequencing and karyotype analyses detected that all the 16 pairs of plantlets analyzed were hybrids, indicating that most endosperm-derived plantlets were allotriploid with a parental chromosome ratio of 2:1 (maternal: paternal). In addition, chloroplast DNA sequencing revealed maternal inheritance in the endosperm-derived plantlets, consistent with embryo-derived plantlets.

CONCLUSIONS

This study is the first to demonstrate the production of allotriploid hybrid plants through endosperm culture using seeds from interspecific crosses, as supported by cellular and genetic analyses. Additionally, the study established a novel system for simultaneously producing diploid and allotriploid hybrids from a single seed, providing valuable materials to study the effects of polyploidization and hybridization in allopolyploid plants. These findings contribute to plant breeding strategies and advance our understanding of hybridization, polyploidization, and allopolyploid plant development.

Insights into the genetic architecture of the reciprocal interspecific hybrids derived from Chrysanthemum dichrum and C. nankingense

Chrysanthemums are versatile ornamental plants, and improving leaf and flower traits is an important breeding objective. Distant hybridization is a powerful method for plant breeding and genetic improvement, whereas the genetic basis in interspecific F1 progeny of chrysanthemums needs to be better understood for breeding purposes. In this study, the leaf and floral traits of the 273 reciprocal interspecific F1 hybrids of diploid C. dichrum (YSJ) and C. nankingense (JHN) were analyzed along with their SNP-derived genetic structure to elucidate the influence of differences in genetic background between the parents on the hybrid performance. We then performed a genome-wide association analysis (GWAS) to reveal the investigated traits' genomic loci and candidate genes. Considerable phenotypic variation (8.81% ~ 55.78%) and heterosis with transgressive segregation in both directions were observed in the reciprocal progenies. We observed a higher level of phenotypic variation in JHN × YSJ rather than in YSJ × JHN. Also, a significant reciprocal effect was observed for most examined traits. Based on the SNP data, we separated the hybrid progenies into three groups (I, II, and III), albeit imperfectly dependent on the cross directions, except for some reciprocal hybrids clustering into group II. Group I from YSJ × JHN and Group III from YSJ × JHN differed with contrasting F ST and π ratios, indicating the genetic changes in the reciprocal populations. The outcome of GWAS via the IIIVmrMLM method detected 339 significant quantitative trait nucleotides (QTNs) and 40 suggestive QTNs, and the phenotypic variation explained by a single QTN ranged from 0.26% to 7.42%. Within 100 kb upstream and downstream of the important QTNs, we discovered 49 known genes and 39 new candidate genes for the investigated leaf and floral traits. Our study provides profound insights into the genetic architecture of reciprocal hybrid progenies of chrysanthemum species, facilitating future breeding activities.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01518-0.

Characterization of chloroplast genome and phylogenetic analysis of the Elaeagnus hybrid variety E. 'viridis' (Elaeagnaceae)

Elaeagnus 'viridis', an artificial hybrid of E. macrophylla (♂) Thunb. (1784) × E. pungens (♀) Thunb. (1784), is known for its economic and ecological value. In this study, we sequenced and assembled the whole chloroplast (cp) genome of E. 'viridis'. The results showed that its cp genome was 152,284 bp long, showing a typical quadripartite structure and containing a large single-copy region (LSC, 82,299 bp), a small single-copy region (SSC, 18,239 bp), and a pair of inverted repeats (IRs, 51,746 bp). The cp genome contains 132 genes, including 86 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 66 common PCGs revealed that E. 'viridis' is most closely related to its maternal parent E. pungens. The chloroplast genomic information reported in this study will shed some useful light for further genetic studies in the genus Elaeagnus.

Novel molecular markers for Taxodium breeding from the chloroplast genomes of four artificial Taxodium hybrids

Taxodium "Zhongshanshan" are a group of intraspecific Taxodium hybrids with superparental dominance and high ecological and economic value in southern China. Identifying the parentage of hybrids, especially the male parent, is critically important for genetic studies. However, the large nuclear genomes of members of the genus Taxodium pose a major challenge for the development of molecular markers. Here, we developed novel molecular markers by conducting a comparative analysis of the chloroplast genomes of four artificial Taxodium hybrids and their parents. The lengths of the whole chloroplast genome ranged from 131,942 to 132,128 bp, and the total guanine (GC) content of the chloroplast genomes ranged from 34.6% to 35.81%. A total of 120 unique genes were identified, including 83 protein-coding genes, 33 transfer RNAs, and four ribosomal RNAs. There were 69-71 simple sequence repeats were detected in the four hybrids. Phylogenetic analysis revealed that these hybrids clustered with their paternal parents. Similar findings were obtained by analysis of the GC content of protein-coding genes. Molecular markers were developed using the highly variable regions of the chloroplast genomes, and polymerase chain reaction (PCR) assays revealed that these markers were effective for identifying the male parents of these hybrids. Our findings indicate for the first time that the chloroplast genomes of Taxodium are paternally inherited. Generally, these molecular markers could facilitate breeding and genetic studies of Taxodium.

Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids

The chloroplast genomic information was obtained from three wild Solanum and four hybrids by chloroplast genome sequencing. The chloroplast genomes of the seven samples comprise of a circular structure and sizes from 155,581 to 155,612 bp and composed of 130 genes. The genome structures of the two hybrids were identical, while the other two hybrids showed 2 bp differences in the LSC when compared with their maternal parent. The total sites of SNP and InDel were 39-344 and 54-90, respectively. With the exception of one hybrid with two additional sites, the other hybrids were identical to their maternal.

Interspecific Hybrids Between Pelargonium × hortorum and Species From P. Section Ciconium Reveal Biparental Plastid Inheritance and Multi-Locus Cyto-Nuclear Incompatibility

The genetics underlying Cyto-Nuclear Incompatibility (CNI) was studied in Pelargonium interspecific hybrids. We created hybrids of 12 closely related crop wild relatives (CWR) with the ornamental P. × hortorum. Ten of the resulting 12 (F₁) interspecific hybrids segregate for chlorosis suggesting biparental plastid inheritance. The segregation ratios of the interspecific F₂ populations show nuclear interactions of one, two, or three nuclear genes regulating plastid function dependent on the parents. We further validated that biparental inheritance of plastids is common in section Ciconium, using diagnostic PCR primers. Our results pave the way for using the diverse species from section Ciconium, each with its own set of characteristics, as novel sources of desired breeding traits for P. × hortorum cultivars.

An Empirical Analysis Rejects the Hybrid Speciation Hypothesis of a Crucial Kiwifruit Species, Despite Genomic Evidence of Frequent Interspecific Gene Flow in the Genus

Hybrid speciation is an important way to generate species diversity. In general, however, interspecific hybridization is easily confused with the formation of hybrid species. Using the genomic resequencing data of the kiwifruit genus (Actinidia), at least ten species were documented recently as homoploid hybrid species, and thus a two-layer mode of species diversification has been proposed. As a crucial piece of evidence, Actinidia fulvicoma was identified as a hybrid derivative of Actinidia eriantha × Actinidia cylindrica, representing a rare case of hybrid species in kiwifruit that won the competition of ecological niches with one of its putative parental species, A. cylindrica. However, the hypothesized hybrid origin of A. fulvicoma is inconsistent with our specimen observations. Here, we present multiple lines of evidence to reject the hybrid speciation hypothesis for this species, despite genomic evidence for frequent interspecific gene flow. We collected the samples of A. fulvicoma in type locality and neighboring regions to contrast them with type specimen, and sequenced nuclear ribosomal DNA ITS, chloroplast trnL-trnF and mitochondrial nad2-i3, as well as four single-copy nuclear genes explored from kiwifruit genomes, to infer phylogenetic relationships among A. fulvicoma, its putative parental species, and their relatives. Our data definitely reveal that A. fulvicoma occupies an independent backbone lineage and it is not a hybrid. This study suggests that correct evolutionary applications on extensive surveys of the putative hybrid and its possible parents with strict criteria are necessary in the documentation of hybrid speciation to advance our understanding of the genomic basis of hybrid species.

Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales)

Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome (mitogenome) from only one fern genus. We developed a new and efficient method to examine plastome and mitogenome inheritance in a fern species-Deparia lancea (Athyriaceae, Aspleniineae, Polypodiales), and found that plastid and mitochondrial DNAs were transmitted from only the maternal parentage to a next generation. To further examine whether both organelle genomes have the same manner of inheritance in other Deparia ferns, we sequenced both plastid and mitochondrial DNA regions of inter-species hybrids, and performed phylogenetic analyses to identify the origins of organellar DNA. Evidence from our experiments and phylogenetic analyses support that both organelle genomes in Deparia are uniparentally and maternally inherited. Most importantly, our study provides the first report of mitogenome inheritance in eupolypod ferns, and the second one among all ferns.

Characterization of Genomic Inheritance of Intergeneric Hybrids between Ascocenda and Phalaenopsis Cultivars by GISH, PCR-RFLP and RFLP

Background

The intergeneric hybrids between Ascocenda John De Biase ‘Blue’ and Phalaenopsis Chih Shang's Stripes have been generated to introduce the blue color into the Phalaenopsis germplasm in prior study. In order to confirm the inheritance in hybrid progenies, genomic in situ hybridization (GISH) and restriction fragment length polymorphism (RFLP) analysis were conducted to confirm the intergeneric hybridization status.

Methods/Results

GISH analysis showed the presence of both maternal and paternal chromosomes in the cells of the putative hybrids indicating that the putative hybrid seedlings were intergeneric hybrids of the two parents. Furthermore, twenty-seven putative hybrids were randomly selected for DNA analysis, and the external transcribed spacer (ETS) regions of nrDNA were analyzed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and RFLP analyses to identify the putative hybrids. RFLP analysis showed that the examined seedlings were intergeneric hybrids of the two parents. However, PCR-RFLP analysis showed bias to maternal genotype.

Conclusions

Both GISH and RFLP analyses are effective detection technology to identify the intergeneric hybridization status of putative hybrids. Furthermore, the use of PCR-RFLP analysis to identify the inheritance of putative hybrids should be carefully evaluated.

High-throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea

Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts.

Why are most organelle genomes transmitted maternally?

Why the DNA-containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall-back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode.

DNA abandonment and the mechanisms of uniparental inheritance of mitochondria and chloroplasts

For most eukaryotic organisms, the nuclear genomes of both parents are transmitted to the progeny following biparental inheritance. For mitochondria and chloroplasts, however, uniparental inheritance (UPI) is frequently observed. The maternal mode of inheritance for mitochondria in animals can be nearly absolute, suggesting an adaptive advantage for UPI. In other organisms, however, the mode of inheritance for mitochondria and chloroplasts can vary greatly even among strains of a species. Here, I review the data on the transmission of organellar DNA (orgDNA) from parent to progeny and the structure, copy number, and stability of orgDNA molecules. I propose that UPI is an incidental by-product of DNA abandonment, a process that lowers the metabolic cost of orgDNA repair.