Paternal inheritance of plastids in interspecific hybrids of the genus Actinidia revealed by PCR-amplification of chloroplast DNA fragments

Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity

Kiwifruits, belonging to the genus Actinidia, are acknowledged as one of the most successfully domesticated fruits in the twentieth century. Despite the rich wild resources and diverse phenotypes within this genus, insights into the genomic changes are still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections of Actinidia, leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.0 to 699.6 Mb. By compiling these haplotype genomes, we constructed a super pan-genome for the genus. We identified numerous structural variations (SVs, including variations in gene copy number) and highly diverged regions in these genomes. Notably, significant SV variability was observed within the intronic regions of the MED25 and TTG1 genes across different materials, suggesting their potential roles in influencing fruit size and trichome formation. Intriguingly, our findings indicated a high genetic divergence between two haplotype genomes, with one individual, tentatively named Actinidia × leiocacarpae, from sect. Leiocacarpae. This likely hybrid with a heterozygous genome exhibited notable genetic adaptations related to resistance against bacterial canker, particularly through the upregulation of the RPM1 gene, which contains a specific SV, after infection by Pseudomonas syringae pv. actinidiae. In addition, we also discussed the interlineage hybridizations and taxonomic treatments of the genus Actinidia. Overall, the comprehensive pan-genome constructed here, along with our findings, lays a foundation for examining genetic compositions and markers, particularly those related to SVs, to facilitate hybrid breeding aimed at developing desired phenotypes in kiwifruits.

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.

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.

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.

Low frequency paternal transmission of plastid genes in Brassicaceae

Plastid-encoded genes are maternally inherited in most plant species. Transgenes located on the plastid genome are thus within a natural confinement system, preventing their distribution via pollen. However, a low-frequency leakage of plastids via pollen seems to be universal in plants. Here we report that a very low-level paternal inheritance in Arabidopsis thaliana occurs under field conditions. As pollen donor an Arabidopsis accession (Ler-Ely) was used, which carried a plastid-localized atrazine resistance due to a point mutation in the psbA gene. The frequency of pollen transmission into F1 plants, based on their ability to express the atrazine resistance was 1.9 × 10(-5). We extended our analysis to another cruciferous species, the world-wide cultivated crop Brassica napus. First, we isolated a fertile and stable plastid transformant (T36) in a commercial cultivar of B. napus (cv Drakkar). In T36 the aadA and the bar genes were integrated in the inverted repeat region of the B. napus plastid DNA following particle bombardment of hypocotyl segments. Southern blot analysis confirmed transgene integration and homoplasmy of plastid DNA. Line T36 expressed Basta resistance from the inserted bar gene and this trait was used to estimate the frequency of pollen transmission into F1 plants. A frequency of <2.6 × 10(-5) was determined in the greenhouse. Taken together, our data show a very low rate of paternal plastid transmission in Brassicacea. Moreover, the establishment of plastid transformation in B. napus facilitates a safe use of this important crop plant for plant biotechnology.

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

The inheritance pattern of chloroplast and mitochondria is a critical determinant in studying plant phylogenetics, biogeography and hybridization. To better understand chloroplast and mitochondrial inheritance patterns in Actinidia (traditionally called kiwifruit), we performed 11 artificial interspecific crosses and studied the ploidy levels, morphology, and sequence polymorphisms of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) of parents and progenies. Sequence analysis showed that the mtDNA haplotypes of F1 hybrids entirely matched those of the female parents, indicating strictly maternal inheritance of Actinidia mtDNA. However, the cpDNA haplotypes of F1 hybrids, which were predominantly derived from the male parent (9 crosses), could also originate from the mother (1 cross) or both parents (1 cross), demonstrating paternal, maternal, and biparental inheritance of Actinidia cpDNA. The inheritance patterns of the cpDNA in Actinidia hybrids differed according to the species and genotypes chosen to be the parents, rather than the ploidy levels of the parent selected. The multiple inheritance modes of Actinidia cpDNA contradicted the strictly paternal inheritance patterns observed in previous studies, and provided new insights into the use of cpDNA markers in studies of phylogenetics, biogeography and introgression in Actinidia and other angiosperms.

Biparental inheritance of plastidial and mitochondrial DNA and hybrid variegation in Pelargonium

Plastidial (pt) and mitochondrial (mt) genes usually show maternal inheritance. Non-Mendelian, biparental inheritance of plastids was first described by Baur (Z Indukt Abstamm Vererbungslehre 1:330–351, 1909) for crosses between Pelargonium cultivars. We have analyzed the inheritance of pt and mtDNA by examining the progeny from reciprocal crosses of Pelargoniumzonale and P. inquinans using nucleotide sequence polymorphisms of selected pt and mt genes. Sequence analysis of the progeny revealed biparental inheritance of both pt and mtDNA. Hybrid plants exhibited variegation: our data demonstrate that the inquinans chloroplasts, but not the zonale chloroplasts bleach out, presumably due to incompatibility of the former with the hybrid nuclear genome. Different distribution of maternal and paternal sequences could be observed in different sectors of the same leaf, in different leaves of the same plant, and in different plants indicating random segregation and sorting-out of maternal and paternal plastids and mitochondria in the hybrids. The substantial transmission of both maternal and paternal mitochondria to the progeny turns Pelargonium into a particular interesting subject for studies on the inheritance, segregation and recombination of mt genes.

Potential Cytoplasmic Inheritance in Wisteria sinensis and Robinia pseudoacacia (Leguminosae)

We examined pollen cells of Wisteria sinensis and Robinia pseudoacacia (Leguminosae) to determine a possible mode for cytoplasmic inheritance in these species. Epifluorescence microscopy revealed distinct mature generative cells. Mature generative cells of W. sinensis were associated with large numbers of punctuated fluorescent signals corresponding to cytoplasmic DNA aggregates, but no fluorescent signals were observed in the generative cells of R. pseudoacacia. Closer examination showed that the punctate fluorescent signals corresponded to plastid but not mitochondrial DNA. These results suggest a strong potential for paternal transmission of the plastid genome in W. sinensis. Electron microscopy confirmed the presence of plastids in the generative cells of W. sinensis and the absence of plastids in R. pseudoacacia cells due to an unequal distribution of plastids during the first pollen mitosis. Mitochondria were present and intact in the mature generative cells of both species. The lack of fluoresced mitochondrial DNA suggests a very low level of mitochondrial DNA in the cells. Immunoelectron microscopy demonstrated that the labeling of mitochondrial DNA in these cells was reduced by nearly 90% during pollen development. Such a dramatic reduction suggests an active degradation of paternal mitochondrial DNA, which may contribute greatly to the maternal inheritance of mitochondria. In short, we found that W. sinensis exhibits a strong potential for paternal transmission of plastids and that both W. sinensis and R. pseudoacacia appear to share the same mechanism for maternal mitochondrial inheritance.

Reticulate evolution in kiwifruit (Actinidia, Actinidiaceae) identified by comparing their maternal and paternal phylogenies

Evolutionary relationships within Actinidia, a genus known for the contrasting mode of inheritance of its plastids and mitochondria, were studied. The phylogenetic analysis is based on chloroplast (cp) and mitochondrial (mt) restriction site and sequence data (matK, psbC-trnS, rbcL, and trnL-trnF for cpDNA; nad1-2/3 and nad4-1/2 for mtDNA). The analysis of cp sequence data confirms the hypothesis that the four currently recognized sections are not monophyletic. The detection of incongruences among phylogenies (mtDNA vs. cpDNA tree) coupled with the detection of intraspecific polymorphisms confirms some of the reticulations previously emphasized, diagnoses new hybridization/introgression events, and provides evidence for multiple origin of at least two polyploid taxa. A number of hybridization/introgression events at the diploid, tetraploid, and possibly hexaploid levels are documented. The extensive reticulate evolution undergone by Actinidia could account for the lack of clear morphological discontinuities at the species level.

Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance

Range-wide variation of maritime pine was studied at maternally inherited and paternally inherited markers (mitochondrial DNA and chloroplast DNA). While chloroplast DNA exhibits the highest diversity, phylogeographic inferences from this marker are blurred by homoplasy and extensive pollen flow. In contrast, the only three mitochondrial haplotypes found provide a clear picture of nonoverlapping areas colonized from different refugia, with no single population having a mixed composition (GST = 1). Comparison of the genetic structure inferred from both organelle genomes allows the investigation of differential seed and pollen dispersal, pointing to pollen, but not seed, dispersal across the Strait of Gibraltar (from Morocco into Iberia). A comparison with already available genetic information, especially that of one of the maritime pine's most threatening insect pests, the bast scale Matsucoccus feytaudi, further completes the picture.

A one-step organelle capture: gynogenetic kiwifruits with paternal chloroplasts

Androgenesis, the development of a haploid embryo from a male nucleus, has been shown to result in the instantaneous uncoupling of the transmission of the organelle and nuclear genomes (with the nuclear genome originating from the male parent only and the organelle genomes from the female parent). We report, for the first time, uncoupling resulting from gynogenesis, in Actinidia deliciosa (kiwifruit), a plant species known for its paternal mode of chloroplast inheritance. After pollen irradiation, transmission of nuclear genes from the pollen parent to the progeny was inhibited, but transmission of the chloroplast genome was not. This demonstrates that plastids can be discharged from the pollen tube into the egg with little or no concomitant transmission of paternal nuclear genes. Such events of opposite inheritance of the organelle and nuclear genomes must be very rare in nature and are unlikely to endanger the long-term stability of the association between the different genomes of the cell. However, they could lead to incongruences between organelle gene trees and species trees and may constitute an alternative to the hybridization/introgression scenario commonly invoked to account for such incongruences.