Cytoplasmic Genomes Research Articles

Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion

BackgroundJasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal (“SP”), double-petal (“DP”), and multi-petal (“MP”). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions.ResultsHere, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, “SP”, “DP”, and “MP-hutou” (“HT”), with PacBio reads and the “HT” chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in “HT”. We identified a 14.3 kb “HT”-specific insertion on Chr7 of the “HT” nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that “DP” and “HT” evolved from “SP”, with “HT” being the most recent derivative of “DP”.ConclusionThe comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.

Visualizing Viral RNA Packaging Signals in Action

Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5′ two-thirds of the gRNA of Satellite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate formation of its T = 1 virus-like particle (VLP). These contacts explain why natural virions only package their positive-sense genomes. Asymmetric cryo-EM reconstructions of these VLPs suggest that interactions occur between amino acid residues in the N-terminal ends of the CP subunits and the gRNA PS loop sequences. The base-paired stems of PSs also act non-sequence-specifically by electrostatically promoting the assembly of CP trimers. Importantly, alterations in PS-CP affinity result in an asymmetric distribution of bound PSs inside VLPs, with fuller occupation of the higher affinity 5′ PS RNAs around one vertex, decreasing to an RNA-free opposite vertex within the VLP shell. This distribution suggests that gRNA folding regulates cytoplasmic genome extrusion so that the weakly bound 3′ end of the gRNA, containing the RNA polymerase binding site, extrudes first. This probably occurs after cation-loss induced swelling of the CP-shell, weakening contacts between CP subunits. These data reveal for the first time in any virus how differential PS folding propensity and CP affinities support the multiple roles genomes play in virion assembly and infection. The high degree of conservation between the CP fold of STNV-1 and those of the CPs of many other viruses suggests that these aspects of genome function will be widely shared.

In Planta Androgenesis (Paternal Origin) in Saacharum X Erianthus Intergeneric Hybrid

The present investigation was carried in crosses made between Saccharum species hybrid clones i.e. Co 419, Co 7201 and Co 7224 (2n = 108-112) and Erianthus arundinaceus viz. IK 76-91 (2n = 60) and IK 76-99 (2n = 60) for introducing better ratoon ability, vigour, wide ecological adaptability, extensive root system, drought and water logging resistance, high biomass and disease resistance into modern sugarcane cultivars during 2020-23 at VSI-Sugarcane Breeding Centre, Amboli. Parental apomixis (paternal origin) has been recently noticed and it is unique in Saccharum X Erianthus intergeneric cross seedlings. A total of fifty-one seedlings were obtained from above three intergeneric crosses and out of these eighteen seedlings were reported as androgenetic seedlings as the female act as a surrogate mother. At the early stages, seed germination of seedlings was found two types i.e., one type resembling Saccharum and other resembling Erianthus with deep purple coloration. Morphologically androgenetic seedlings were similar to the male parents IK 76-91 and IK 76-99 with tall large tufted grass like clumps, vegetative stem with thick reproductive buds, root zone narrow and only one row of root eyes, the lamina gradually passes into leaf sheath with no auricle and dewlaps. Cytological studies were made in these seedlings and during metaphase the somatic chromosome number was observed to be 2n = 60 rather than expected 2n = 84-90. This paternal origin may be due to the ability of Erianthus male gametes to produce an embryo within the seed tissues of Saccharum species hybrids but without genetic contribution of the seed. Thus, in planta androgenesis is achieved through the combination of embryogenic behavior of male gametes which has entered in the ovule and the ability of ovules to act as a surrogate mother. They could derive either from the fusion of two male gametes or from the early natural diplodization of the haploid embryo. Such homozygous true breeding seedlings of Saccharum X Erianthus with hybrid vigour are extremely important in crop improvement. This system provides an unparalleled opportunity to shorten the breeding cycle and fix agronomic traits in the homozygous state. These androgenetic plants with Saccharum cytoplasm and Erianthus genome are male sterile making them highly useful for further hybridization and sugarcane improvement programme.

Circular genetic structure of the Abies nephrolepis species complex shaped by the circular landform of Northeast Asia

AbstractAimPinaceae have been noted for their tendency towards reticulation as a result of interspecific hybridization. Here, we demonstrated the phylogeographic dynamics of the native Northeast Asian sub‐alpine conifer, Abies nephrolepis species complex (ANSC), evolving in circular overlaps along the Northeast Asian landform, which functions as a corridor with the sea, thus acting as a geographic barrier.LocationNortheast Asia: the Korean Peninsula, Japanese Archipelago, Russian Far East and northeastern China.TaxonAbies nephrolepis species complex (Family Pinaceae, Genus Abies, Section Balsamea, Abies nephrolepis, A. koreana, A. veitchii and A. sachalinensis).MethodsA total of 728 individuals from 38 ANSC populations were analysed using multiplexed inter‐simple sequence repeat genotyping by sequencing to capture variations in biparental nuclear genomes. Eight mitochondrial regions and eight chloroplast regions of each individual were sequenced using the MiSeq platform and Sanger sequencing. Species distribution models were generated.ResultsBayesian clustering with 507 nuclear single nucleotide polymorphisms and the discrepancy between cytoplasmic and nuclear genome lineages implied contemporary and ancient connections between neighbouring species in the form of circular overlap. This genetic connectivity was supported by principal component analysis. Strong correlations between genetic distance and geographic distance were observed, suggesting that gene flow occurs through a continuous chain around the sea. We also found that gene flow direction and intensity changed over time, with support from palaeodistribution modelling.ConclusionPast hybridization events were captured in cytoplasmic genomes, generating heterogeneity across maternal ancestries. This intensive phylogeographic study demonstrates speciation with incomplete reproductive isolation (continuous gene flow) among neighbouring species with an alteration of the direction and intensity of gene flow due to climate change. The divergence of ANSC due to repeated isolation and reconnection caused by heterogenous physiological environments and climate fluctuation provides a model to solve evolutionary scenarios for reticulate evolution in Pinaceae and other plants.

Cytoplasmic genome contributions to domestication and improvement of modern maize

BackgroundStudies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been systematically investigated.ResultsHere we report co-selection and convergent evolution between nuclear and cytoplasmic genomes by analyzing whole genome sequencing data of 630 maize accessions modern maize and its relatives, including 24 fully assembled mitochondrial and chloroplast genomes. We show that the NB cytotype is associated with the expansion of modern maize to North America, gradually replaces the fertile NA cytotype probably through unequal division, and predominates in over 90% of modern elite inbred lines. The mode of cytoplasmic evolution is increased nucleotypic diversity among the genes involved in photosynthesis and energy metabolism, which are driven by selection and domestication. Furthermore, genome-wide association study reveals correlation of cytoplasmic nucleotypic variation with key agronomic and reproductive traits accompanied with the diversification of the nuclear genomes.ConclusionsOur results indicate convergent evolution between cytoplasmic and nuclear genomes during maize domestication and breeding. These new insights into the important roles of mitochondrial and chloroplast genomes in maize domestication and improvement should help select elite inbred lines to improve yield stability and crop resilience of maize hybrids.

Heterosis for Resistance to Insect Herbivores in a 3-Line Hybrid Rice System.

Three-line hybrid rice is produced by crossing male sterile (A line) rice with a fertility-restorer (R line). Fertile lines (B lines) are also required to maintain A line seed for breeding programs. We used a range of hybrids and their parental lines to assess the frequency and nature of heterosis for resistance to the whitebacked planthopper (Sogatella furcifera), brown planthopper (Nilaparvata lugens) and yellow stemborer (Scirpophaga incertulas). Heterosis is defined as trait improvement above the average of the parental lines as a result of outbreeding. Based on the results from a greenhouse study that challenged hybrids and their parental lines with each herbivore species, we found that susceptibility to planthoppers was associated with one of the eight A lines tested, but resistance was improved by crossing with a relatively resistant restorer. Higher frequencies of heterosis for susceptibility in comparisons between hybrids and their B lines suggest that susceptibility was not related to the cytoplasmic genomes of the associated sterile A lines. Furthermore, because none of the parental lines possessed currently effective resistance genes, improved resistance against planthoppers was probably due to quantitative resistance. In a related field trial, hybrids had generally higher yields than their fertile parents and often produced larger grain; however, they were often more susceptible to stemborers, leaffolders (Cnaphalocrocis medinalis) and other caterpillars (Rivula atimeta). This was largely a consequence of hybrid heterosis for plant biomass and was strongly affected by crop duration. We make a series of recommendations to improve hybrid breeding to reduce the risks of herbivore damage.

Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U.

The interaction and coevolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, 2 billion yr later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance versus cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features 3 diploid species that together have formed 3 separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in Brassica carinata (BBCC) and 2 varieties of Brassica juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these 2 separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the Brassica nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.

Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids.

The parent-of-origin effect on seeds can result from imprinting (unequal expression of paternal and maternal alleles) or combinational effects between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding factors, we produced cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in Arabidopsis (Arabidopsis thaliana) ecotypes Col-0 and C24. These CNS lines differed only in the nuclear genome (imprinting) or cytoplasm. The CNS reciprocal hybrids with the same cytoplasm displayed ∼20% seed size difference, whereas the seed size was similar between the reciprocal hybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection identified 104 maternally expressed genes (MEGs) and 90 paternally expressed genes (PEGs). These imprinted genes were involved in pectin catabolism and cell wall modification in the endosperm. Homeodomain Glabrous9 (HDG9), an epiallele and one of 11 cross-specific imprinted genes, affected seed size. In the embryo, there were a handful of imprinted genes in the CNS hybrids but only 1 was expressed at higher levels than in the endosperm. AT4G13495 was found to encode a long-noncoding RNA (lncRNA), but no obvious seed phenotype was observed in lncRNA knockout lines. Nuclear RNA Polymerase D1 (NRPD1), encoding the largest subunit of RNA Pol IV, was involved in the biogenesis of small interfering RNAs. Seed size and embryos were larger in the cross using nrpd1 as the maternal parent than in the reciprocal cross, supporting a role of the maternal NRPD1 allele in seed development. Although limited ecotypes were tested, these results suggest that imprinting and the maternal NRPD1-mediated small RNA pathway play roles in seed size heterosis in plant hybrids.

Comparative Study of Plastomes in Solanum tuberosum with Different Cytoplasm Types

The potato is one of the most important food crops in the world. Improving the efficiency of potato breeding is of great importance for solving the global food problem. Today, researchers distinguish between six potato cytoplasm types: A, M, P, T, W, D. In the current study, the complete chloroplast genomes of Solanum tuberosum accessions with five out of the six major cytoplasmic genome types were sequenced (T-, W-, D-, A-, and P-genomes). A comparative analysis of the plastomes in potato accessions with different cytoplasm types was carried out for the first time. The time of origin of the different cytoplasm types was estimated. The presence of two main groups of chloroplast genomes among cultivated potato was confirmed. Based on the phylogenetic analysis of the complete plastome sequences, five main evolutionary branches of chloroplast genomes can be distinguished within the Petota section. Samples with A- and P- cytoplasm formed isolated and distant groups within a large and polymorphic group of samples with M-type cytoplasm, suggesting that A and P genomes arose independently. The findings suggest that the diversity of the T-genome in S. tuberosum Group Tuberosum could be initially low due to a bottle neck already existing at the origin of the Chilean clade. Differences in the rbcL gene sequence may be one of the factors causing differences in economically important traits in species with A and T-type cytoplasm. The data obtained will contribute to the development of methods for molecular marking of cytoplasm types and increase knowledge about the evolution and diversity of potato.

Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad (Diplotaxis spp.) Species.

Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 Diplotaxis species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between trnL and trnF and tRNA-Phe gene (trnL-F), the rubisco (rbcl), the maturase K (matk), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. A highly polymorphic marker (HRM500) derived from a comparison of cytoplasmic genome sequences in Brassicaceae, was also included. Subsequently, a real-time PCR method coupled with HRM analysis was implemented to better resolve taxonomic relationships and identify assays suitable for species identification. Integration of the five barcode regions revealed a grouping of the species according to the common chromosomal set number. Clusters including species with n = 11 (D. duveryrieriana or cretacea, D. tenuifolia, D. simplex and D. acris), n = 8 (D. ibicensis, D. brevisiliqua and D. ilorcitana), and n = 9 (D. brachycarpa, D. virgata, D. assurgens, and D. berthautii) chromosomes were identified. Both phylogenetic analysis and the genetic structure of the collection identified D. siifolia as the most distant species. Previous studies emphasized this species' extremely high glucosinolate content, particularly for glucobrassicin. High-resolution melting analysis showed specific curve patterns useful for the discrimination of the species, thus determining ITS1 as the best barcode for fingerprinting. Findings demonstrate that the approach used in this study is effective for taxa investigations and genetic diversity studies.

Intracellular gene transfer and codon usage of cytoplasmic genomes in green plants

Abstract Intracellular gene transfer is widely recognized as one of the most important driving forces for species evolution. Here we investigated transferred cytoplasmic motifs in green plants including spore-bearing plants and seed-bearing plants (hereafter termed spore plants and seed plants) . Our analyses revealed that gene transfer in spore plants was characterized by shorter motifs than that of seed plants. Several spore species did not exhibit intracellular gene transfer. Meanwhile, high frequency transferred tRNA genes were identified with average values of minimum free energy at moderate level. From the chloroplast to the mitochondrial genome, trnP was found to have transferred with high frequency in green plants. In gene transfer from the mitochondrial to the chloroplast genome, trnN was found to be a highly transferred gene. We observed that several tRNA genes including trnF, trnW, and trnN were involved in bidirectional transfer, which may be related to application strategy of functional protein-coding genes in a plant’s adaptive evolution. Codon Adaptation Index (CAI) analysis showed that codon usage was unbalanced in spore and seed plants. CAI values for seed plants were higher than those for spore plants in general, which may reveal rapid divergence adaptability of codon usage in the former. These results provide novel insights into gene transfer and codon usage within cytoplasmic genomes.

A study on the adaptive potential of new sterile cytoplasm of Beta patula and Beta maritima L. from wild beets of the genus Beta L.: cold resistance and traits of early sugar accumulation in introduced alloplasmic lines

Purpose. Assessment of new sugar beet breeding genotypes by a set of economically valuable traits to determine their suitability for the efficiency of the process of managing the production of bioethanol with the study of the activity of photosynthesis according to the content of chlorophylls a and b, early accumulation of carbohydrates, tolerance to low temperatures, germination of apozygous seeds and using new plasma of the substituted lines of sugar beet with introduced sterile cytoplasms from wild species Beta patula and B. maritima L. and apozygous lines A9 with S vulgaris Owen's cytoplasm. Methods. Field methods were used (pollen-free regime for the reproduction of apozygotic seeds in conditions of isolation and seed monogermity of the seed plants), laboratory methods (selection of the best experimental genotypes for cold resistance, analysis of productivity and dynamics of carbohydrate accumulation). Results. Self-fertile pollen-sterile lines A9 Beta vulgaris Sxxzz rr with an apomictic method of seed reproduction of seeds (Yaltushkiv EBS) and commercial hybrids with early carbohydrate accumulation were selected for the recessive colour of the hypocotyl r-r- and gametophytic reduced parthenogenesis for hybridization according to the scheme: A9 Beta vulgaris Sxxzz rr × Beta vulgaris Mm Rr. The influence of cytoplasmic inheritance of B. maritima and B. patula on cold resistance indicators was studied and seed samples of the experimental genotypes No. 17225, 17221, 17222, 17220, 17226, 17223 were selected among substituted lines with seed germination rates at +4°C varying from 14.3 to 40.3%. Experimental genotypes of the substituted lines, grown in the conditions of pots were selected and examined by the indicators of early accumulation of sugars, which had values from 16.2 to 17.6% during four months of vegetation; photosynthetic activity with indicators of the content of chlorophyll varying from 2.06 to 1.32%, and chlorophyll b from 1.02 to 0.65%. Conclusions. Sugar beet hybrids, created with the use of cold-resistant substituted pollen-sterile lines of sugar beet, thanks to the natural evolution of the introduced cytoplasmic genome, ensure the extension of the growing season, high productivity, early accumulation of sugars and enrichment of the crop adaptation potential. The article contains the results of the study of the early carbohydrate accumulation, photosynthetic activity of selected experimental genotypes of the substituted sugar beet lines with high seed quality and 100% monogermity. Root crops of apomictic lines were selected based on R+r hypocotyl colour, generative reduced parthenogenesis, and studied for their specifics of seed set under the pollen-free regime.

Sex Without Sexes: Can the Cost of Finding a Mate Explain Diversity in Fungal Mating Systems?

Eukaryotes have evolved myriad ways of uniting gametes during sexual reproduction. A repeated pattern is the convergent evolution of a mating system with the fusion of larger gametes with smaller gametes (anisogamy) from that of fusion between morphologically identical gametes (isogamy). In anisogamous species, sexes are defined as individuals that produce only one gamete type. Although sexes abound throughout Eukarya, in fungi there are no biological sexes, because even in anisogamous species, individuals are hermaphroditic and produce both gamete types. For this reason, the term mating types is preferred over sexes, and, thus defined, only individuals of differing mating types can mate (homoallelic incompatibility). In anisogamous fungal species, there is scant evidence that there are more than two mating types, and this may be linked to genetic constraints, such as the use of mating types to determine the inheritance of cytoplasmic genomes. However, the mushroom fungi (Agaricomycetes) stand out as having both large numbers of mating types within a species, which will allow nearly all individuals to be compatible with each other, and reciprocal exchange of nuclei during mating, which will avoid cytoplasmic mixing and cyto-nuclear conflicts. Although the limitation of mating types to two in most fungi is consistent with the cyto-nuclear conflicts model, there are many facets of the Agaricomycete life cycle that also suggest they will demand a high outbreeding efficiency. Specifically, they are mostly obligately sexual and outcrossing, inhabit complex competitive niches, and display broadcast spore dispersal. Subsequently, the Agaricomycete individual pays a high cost to being choosy when encountering a mate. Here, I discuss the costs of mate finding and choice and demonstrate how most fungi have multiple ways of reducing these costs, which can explain why mating types are mostly limited to two per species. Nevertheless, it is perplexing that fungi have not evolved multiple mating types on more occasions nor evolved sexes. The few exceptions to these rules suggest that it is dictated by both molecular and evolutionary constraints.

A tale of two genomes: What drives mitonuclear discordance in asexual lineages of a freshwater snail?

We use genomic information to tell us stories of evolutionary origins. But what does it mean when different genomes report wildly different accounts of lineage history? This genomic "discordance" can be a consequence of a fascinating suite of natural history and evolutionary phenomena, from the different inheritance mechanisms of nuclear versus cytoplasmic (mitochondrial and plastid) genomes to hybridization and introgression to horizontal transfer. Here, we explore how we can use these distinct genomic stories to provide new insights into the maintenance of sexual reproduction, one of the most important unanswered questions in biology. We focus on the strikingly distinct nuclear versus mitochondrial versions of the story surrounding the origin and maintenance of asexual lineages in Potamopyrgus antipodarum, a New Zealand freshwater snail. While key questions remain unresolved, these data inspire multiple testable hypotheses that can be powerfully applied across a broad range of taxa toward a deeper understanding of the causes and consequences of mitonuclear discordance, the maintenance of sex, and the origin of new asexual lineages.

A male-killing gene encoded by a symbiotic virus of Drosophila

In most eukaryotes, biparentally inherited nuclear genomes and maternally inherited cytoplasmic genomes have different evolutionary interests. Strongly female-biased sex ratios that are repeatedly observed in various arthropods often result from the male-specific lethality (male-killing) induced by maternally inherited symbiotic bacteria such as Spiroplasma and Wolbachia. However, despite some plausible case reports wherein viruses are raised as male-killers, it is not well understood how viruses, having much smaller genomes than bacteria, are capable of inducing male-killing. Here we show that a maternally inherited double-stranded RNA (dsRNA) virus belonging to the family Partitiviridae (designated DbMKPV1) induces male-killing in Drosophila. DbMKPV1 localizes in the cytoplasm and possesses only four genes, i.e., one gene in each of the four genomic segments (dsRNA1−dsRNA4), in contrast to ca. 1000 or more genes possessed by Spiroplasma or Wolbachia. We also show that a protein (designated PVMKp1; 330 amino acids in size), encoded by a gene on the dsRNA4 segment, is necessary and sufficient for inducing male-killing. Our results imply that male-killing genes can be easily acquired by symbiotic viruses through reassortment and that symbiotic viruses are hidden players in arthropod evolution. We anticipate that host-manipulating genes possessed by symbiotic viruses can be utilized for controlling arthropods.

Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination.

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of the mitochondrial genome architecture and recombination. We used PacBio sequencing to reassemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by an assembly of short reads and likely corresponding to a large noncoding region commonly present in the mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy (LSC) region and a small single-copy (SSC) region separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of a "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between single-nucleotide polymorphisms in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.

Seed productivity of alloplasmic lines of Beta patula and B. maritima with sterile cytoplasm under the conditions of apozygotic reproduction

Purpose. Revealing the effect of the cytoplasmic genome of replaced lines with the plasma of wild species Beta patula and B. maritima L., and apozygotic lines A4–A8 with the cytoplasm of S vulgaris Owen on the main factors of apozygotic reproduction, seed productivity, germination, monogermity and sterility as affected by the genetic origin of breeding material.
 Methods. The research was carried out in the Cytogenetics Laboratory (IBCSB), the Laboratory for Apomixis and Polyploidy of the Yaltushkiv EBS, and the Laboratory for Adaptive Breeding (Veselyi Podil EBS). Apozygotic seeds were obtained under a pollen-free regime according to the IBCSB’s Methods for Spatial Isolation and Parchment Insulators. Each seed bearer plant phenotype was determined during the flowering period by pollen sterility and partial flowering. Classification of plants was performed according to Owen (1945), with identifying plants of CMS-0, Type CMS-1, and CMS-2 types. The Monogermity of seed plants was assessed visually by the presence of separate fruits on the central shoots. In 2021, the roots of the replaced lines of the Veselyi Podil EBS were planted under the conditions of a pollen-free regime in the experimental field of the IBCSB. Seed production under apozygositic conditions was studied, taking into account the number of set fruits per 10-cm segment with 5 replications for each seed bearer. Germination was determined on the 10th day and germination vigour on the 5th day.
 Results. New sources of cytoplasmic male sterility (CMS) were obtained in the cytogenetics laboratory based on a genetic model of crossbreeding analysis, using differentiation and tools according to the marker-linked genes of hypocotyl color R+r-, and one / two-year development cycle B+b-. The analyzers for the nature of sugar beet sterility were sterility maintainers, dominant homozygotes for recessive genes of anthocyanin color, development cycle, partial fertility and sterility (NBeta vulgaris Sxxzz rr bb). Monogerm pollen-sterile lines with an apomictic way of seed reproduction (Yaltushkiv EBS) (A4–A8 Beta vulgaris Sxxzz rr), selected for the dominant color of the hypocotyl R+r-, stabilized for the trait of monogermity, 100% sterility and 2x gene ploidy, were characterized by low seed productivity. High rates of apozygotic seed development (80 to 96.4% of the number of set flowers) were observed against the background of the sterile cytoplasm of Beta maritima (Turkey). In the CMS BC4S patula line, the number of set apozygotic seeds ranges from 34 ± 0.3 to 39 ± 0.42, and the indicators of degenerated flowers under apozygotic regime varied from 31.2 to 54.3%. Isolated were seed plants with high self-reproduction, such as BC4S maritima Turkey, k.2/1, k.6/2, k.6/3 and k.3/4, k.9/4 on the background of new plasma of wild species of B. patula. The phenomenon of high self-reproduction of seeds (up to 98.5−96.4% of set flowers) was detected in line 21-011 CHS BC5S patula, which was comparable with hybrids and sterility maintainers (97.5−93.1%), which is determined by a special interaction of the beet nuclear genome of sugar beet and new plasma of wild species of the genus Beta L.
 Conclusions. The apomictic way of seed reproduction ensures the shortening of the breeding scheme for sugar beet due to high seed reproduction of mother parent in substituted lines with new plasma and differentiation by gametophytic reduction of parthenogenesis using morphological marker traits.

Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance.

Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. Although uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but the recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which led to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism, and the emergence of reproductive isolation.

Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification

Although interactions between the cytoplasmic and nuclear genomes occurred during diversification of many plants, the evolutionary conflicts due to cytonuclear interactions are poorly understood in crop breeding. Here, we constructed a pan-mitogenome and identified chimeric open reading frames (ORFs) generated by extensive structural variations (SVs). Meanwhile, short reads from 184 accessions of citrus species were combined to construct three variation maps for the nuclear, mitochondrial, and chloroplast genomes. The population genomic data showed discordant topologies between the cytoplasmic and nuclear genomes because of differences in mutation rates and levels of heteroplasmy from paternal leakage. An analysis of species-specific SVs indicated that mitochondrial heteroplasmy was common and that chloroplast heteroplasmy was undetectable. Interestingly, we found a prominent divergence in the mitogenomes and the highest genetic load in the, which may provide the basis for cytoplasmic male sterility (CMS) and thus influence the reshuffling of the cytoplasmic and nuclear genomes during hybridization. Using cytoplasmic replacement experiments, we identified a type of species-specific CMS in mandarin related to two chimeric mitochondrial genes. Our analyses indicate that cytoplasmic genomes from mandarin have rarely been maintained in hybrids and that paternal leakage produced very low levels of mitochondrial heteroplasmy in mandarin. A genome-wide association study (GWAS) provided evidence for three nuclear genes that encode pentatricopeptide repeat (PPR) proteins contributing to the cytonuclear interactions in the Citrus genus. Our study demonstrates the occurrence of evolutionary conflicts between cytoplasmic and nuclear genomes in citrus and has important implications for genetics and breeding.

Salt tolerance QTLs of an endemic rice landrace, Horkuch at seedling and reproductive stages

Salinity has a significant negative impact on production of rice. To cope with the increased soil salinity due to climate change, we need to develop salt tolerant rice varieties that can maintain their high yield. Rice landraces indigenous to coastal Bangladesh can be a great resource to study the genetic basis of salt adaptation. In this study, we implemented a QTL analysis framework with a reciprocal mapping population developed from a salt tolerant landrace Horkuch and a high yielding rice variety IR29. Our aim was to detect genetic loci that contributes to the salt adaptive responses of the two different developmental stages of rice which are very sensitive to salinity stress. We identified 14 QTLs for 9 traits and found that most are unique to specific developmental stages. In addition, we detected a significant effect of the cytoplasmic genome on the QTL model for some traits such as leaf total potassium and filled grain weight. This underscores the importance of considering cytoplasm-nuclear interaction for breeding programs. Finally, we identified QTLs co-localization for multiple traits that highlights the possible constraint of multiple QTL selection for breeding programs due to different contributions of a donor allele for different traits.