RPS2 Research Articles

Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes

BackgroundGene transfer between the organelles and the nucleus plays a central role in shaping plant genome evolution. The identification and analysis of nuclear DNA of plastid (NUPTs) and mitochondrial (NUMTs) origins are important for exploring the extent of intracellular DNA transfer in genomes.ResultsWe report the complete plastid and mitochondrial genomes (plastome and mitogenome) of Cicuta virosa (Apiaceae) as well as a draft nuclear genome using high-fidelity (HiFi) PacBio sequencing technologies. The C. virosa plastome (154,449 bp) is highly conserved, with a quadripartite structure, whereas the mitogenome (406,112 bp) exhibits two chromosomes (352,718 bp and 53,394 bp). The mitochondrial-encoded genes (rpl2, rps14, rps19, and sdh3) were successfully transferred to the nuclear genome. Our findings revealed extensive DNA transfer from organelles to the nucleus, with 6,686 NUPTs and 6,237 NUMTs detected, covering nearly the entire plastome (99.93%) and a substantial portion of the mitogenome (77.04%). These transfers exhibit a range of sequence identities (80–100%), suggesting multiple transfer events over evolutionary timescales. Recent DNA transfer between organelles and the nucleus is more frequent in mitochondria than that in plastids.ConclusionsThis study contributes to the understanding of ongoing genome evolution in C. virosa and underscores the significance of the organelle-nuclear genome interplay in plant species. Our findings provide valuable insights into the evolutionary processes that shape organelle genomes in Apiaceae, with implications for broader plant genome evolution.

Dynamic changes in RNA integrity, gene expression, and tissue pathomorphology of experimental mice in the postmortem period

Aim. To examine the pattern of morphological changes, RNA quality number, and gene expression in mouse tissues sampled at autopsy under controlled experimental conditions.Materials and methods. Balb/c mice were euthanized and subsequently subjected to necropsy at 0, 3, 12, 24, 48, and 72 hours of the postmortem period. During the first three hours following euthanasia, the mice were maintained at room temperature, after which they were transferred to a refrigerator (4 º С). Total RNA was extracted from tissue samples taken from the kidney, liver, and brain; the integrity of the RNA samples was assessed by capillary electrophoresis, and the RNA quality number (RQN) was calculated. The expression levels of Actb, Epas1, and Rps18 housekeeping genes were evaluated by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) with original primers and probes using the TaqMan assay. The histologic examination was performed according to standard techniques.Results. Degradation of RNA extracted from mouse kidney tissues appeared to be greater than that of RNA taken from the liver. In the meantime, a negative linear correlation was observed between RQN and the duration of the postmortem interval for liver and kidney samples. In contrast, no significant changes in the RQN score were observed for brain RNA samples at any of the time points. The expression of the Epas1 and Rps18 genes was significantly decreased in mouse kidney and liver tissues. However, the level of Epas1 and Rps18 gene expression in the brain remained stable at all time points and did not exhibit a significant decrease at 72 hours after euthanasia. No obvious morphological changes were detected by the histologic examination, which does not exclude the presence of ultrastructural pathological changes.Conclusion. RQN in autopsy tissues serves as a crucial predictor of sample quality for molecular biology studies, including gene expression analysis.

Multi-omics analysis in inclusion body myositis identifies mir-16 responsible for HLA overexpression

BackgroundInclusion Body Myositis is an acquired muscle disease. Its pathogenesis is unclear due to the co-existence of inflammation, muscle degeneration and mitochondrial dysfunction. We aimed to provide a more advanced understanding of the disease by combining multi-omics analysis with prior knowledge. We applied molecular subnetwork identification to find highly interconnected subnetworks with a high degree of change in Inclusion Body Myositis. These could be used as hypotheses for potential pathomechanisms and biomarkers that are implicated in this disease.ResultsOur multi-omics analysis resulted in five subnetworks that exhibit changes in multiple omics layers. These subnetworks are related to antigen processing and presentation, chemokine-mediated signaling, immune response-signal transduction, rRNA processing, and mRNA splicing. An interesting finding is that the antigen processing and presentation subnetwork links the underexpressed miR-16-5p to overexpressed HLA genes by negative expression correlation. In addition, the rRNA processing subnetwork contains the RPS18 gene, which is not differentially expressed, but has significant variant association. The RPS18 gene could potentially play a role in the underexpression of the genes involved in 18 S ribosomal RNA processing, which it is highly connected to.ConclusionsOur analysis highlights the importance of interrogating multiple omics to enhance knowledge discovery in rare diseases. We report five subnetworks that can provide additional insights into the molecular pathogenesis of Inclusion Body Myositis. Our analytical workflow can be reused as a method to study disease mechanisms involved in other diseases when multiple omics datasets are available.

Characterization of differentiating lines of phytophthora in soybean

AbstractThe objective of this study was the characterization of commercial cultivars, differentiating lines/cultivars of Phytophthora sojae carrying Rps (resistance Phytophthora Sojae) genes, inoculated with different pathotypes. Thirty‐one differentiating soybeans (Glycine max (L.) Merrill) lines/cultivars carrying Rps genes and six commercial cultivars were evaluated for virulence pattern to PS2.4, PS14.4, PS36.1, PS34.1, and CMES1608 pathotypes. Inoculations were performed using the toothpick technique, with reaction evaluation about 15 days after infection, where the number of healthy, infected, and dead seedlings was quantified. There was a difference in resistance for the pathotypes, and the most virulent were PS34.1 and PS36.1. The Rps1k, Rps11, and Rp12 genes deserve to be highlighted by resistance to the PS34.1 pathotype and the Rps1k, Rps11, Rp12, and Rps8 genes to the PS36.1 pathotype. The line L77‐1863 (Rps1b) showed resistance to the PS2.4 and PS14.4 pathotypes. The characterization of the genotypes allowed the updating of information about them and the identification of new possibilities of resistance sources.

Complete mitochondrial genome sequencing and phylogenetic analysis of Phellinus igniarius

The mitochondrial whole genome of Phellinus igniarius was sequenced with the objective of examining the evolutionary relationships amongst related species. The entire mitochondrial genome was assembled using Illumina sequencing technology. The structural annotation and bioinformatics analysis were performed. The mitochondrial genome is a double-stranded circular DNA molecule with a total length of 172,449 bp and 86 genes, comprising 51 protein-coding genes (PCGs), 33 transport RNA (tRNA) genes, and 2 ribosomal RNA genes. Almost all protein coding genes utilise the ATG start codon, mainly TAA and TAG as the stop codon. 51 PCGs were predominantly affected by purification selection, among which giy-3, giy-6, rps3, lagli-3, lagli-5, lagli-11 and lagli-17 genes contained positive selection sites. Insertions, deletions and mutations were observed in the tRNA gene. With the exception of trnS2, which lacks dihydrouracil arm, the secondary structure of all tRNAs shows a typical clover structure. According to the phylogenetic study, Inonotus obliquus and the Phellius igniarius were closely related, belong to Hymenochaetaceae.

Genome-Wide Association Study for Resistance to Phytophthora sojae in Soybean [Glycine max (L.) Merr.

Phytophthora sojae (Kauffman and Gerdemann) is an oomycete pathogen that threatens soybean (Glycine max L.) production worldwide. The development of soybean cultivars with resistance to this pathogen is of paramount importance for the sustainable management of the disease. The objective of this study was to identify genomic regions associated with resistance to P. sojae isolate 40468 through genome-wide association analyses of 983 soybean germplasms. To elucidate the genetic basis of resistance, three statistical models were employed: the compressed mixed linear model (CMLM), Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK), and fixed and random model circulating probability unification (FarmCPU). The three models consistently identified a genomic region (3.8-5.3 Mbp) on chromosome 3, which has been previously identified as an Rps cluster. A total of 18 single nucleotide polymorphisms demonstrated high statistical significance across all three models, which were distributed in eight linkage disequilibrium (LD) blocks within the aforementioned interval. Of the eight, LD3-2 exhibited the discernible segregation of phenotypic reactions by haplotype. Specifically, over 93% of accessions with haplotypes LD3-2-F or LD3-2-G displayed resistance, whereas over 91% with LD3-2-A, LD3-2-C, or LD3-2-D exhibited susceptibility. Furthermore, the BLINK and FarmCPU models identified new genomic variations significantly associated with the resistance on several other chromosomes, indicating that the resistance observed in this panel was due to the presence of different alleles of multiple Rps genes. These findings underscore the necessity for robust statistical models to accurately detect true marker-trait associations and provide valuable insights into soybean genetics and breeding.

Intracellular gene transfer (IGT) events from the mitochondrial genome to the plastid genome of the subtribe Ferulinae Drude (Apiaceae) and their implications

BackgroundIntracellular gene transfer (IGT) is a phenomenon in genome evolution that occurs between the nuclear and organellar genomes of plants or between the genomes of different organelles. The majority of the plastid genomes (plastomes) in angiosperms have a conserved structure, but some species exhibit unexpected structural variations.ResultsIn this study, we focused on the Ferulinae, which includes Ferula, one of the largest genera in the Apiaceae family. We discovered IGTs in the rps12-trnV IGS region of the plastome’s inverted repeat (IR). We found that partial mitochondrial genome (mitogenome) sequences, ranging in length from about 2.8 to 5.8 kb, were imported into the plastome. In addition to these, that are known from other Scandiceae subtribes, the Ferulinae plastomes contained two unique mitogenome sequences. We have named these sequences Ferula Mitochondrial Plastid sequences (FeMP). FeMP1 varies in length from 336 bp to 1,100 bp, while FeMP2 ranges from 50 bp to 740 bp in length, with the exception of F. conocaula and F. kingdon-wardii, which do not possess FeMP2. Notably, FeMP2 includes a complete rps7 gene of mitogenome origin. In the maximum likelihood (ML) tree constructed from 79 protein-coding genes, Ferulinae appears as a monophyletic group, while Ferula shows paraphyly. Dorema and Fergania are nested within the Ferula clade, sharing the unusual characteristics of the Ferula plastome. Based on these findings, a reclassification of Dorema and Fergania is warranted.ConclusionsOur results shed light on the mechanism of plastome evolution in the Scandiceae with a focus on the unique plastome structure found in the Apiaceae. These findings enhance our understanding of the evolution of plant organellar genomes.

Analysis of Phenolic Compounds of Reynoutria sachalinensis and Reynoutria japonica Growing in the Russian Far East.

The Russian Far East is a region of unique biodiversity, with numerous plant species, including Reynoutria japonica and Reynoutria sachalinensis. These plants are considered a serious threat to biodiversity and are classified as threatened species. However, Reynoutria plants synthesize and accumulate a variety of metabolites that are valued for their positive effects on human health. The main objective of this study is to quantitatively and qualitatively evaluate the content of secondary metabolites in different parts of R. japonica and R. sachalinensis plants. In this study, the results of phylogenetic analysis of the ITS2, matK, and rps16 genes showed that samples collected in the Sakhalin region were closest to R. sachalinensis, while samples collected in Primorsky krai were closer to R. japonica. The high-performance chromatography and mass spectrometry (HPLC-MS/MS) method was used to identify the compounds. As a result of the identification of metabolites in the leaves, stem, and roots of R. japonica and R. sachalinensis, we showed the presence of a total of 31 compounds, including stilbenes, phenolic acids, flavan-3-ols, flavones and flavonols, naphthalene derivatives, anthraquinones and derivatives, and phenylpropanoid disaccharide esters. The root of R. japonica was shown to be a rich source of stilbenes (up to 229.17 mg/g DW), which was 8.5 times higher than that of R. sachalinensis root (up to 27.04 mg/g DW). The root also contained high amounts of emodin derivatives and vanicoside B. Quercetin and its derivatives were the major metabolites in the leaves and stems of both Reynoutria species. In R. japonica leaves, quercetin-3-O-pentoside was the major compound, reaching a total of 7 mg/g DW, accounting for 34% of all compounds analyzed. In contrast, in R. sachalinensis leaves, quercitrin was the major compound (up to 13.96 mg/g DW), accounting for 62% of all compounds and 12.7 times higher than in R. japonica leaves. In turn, R. japonica leaves also contained high amounts of phenolic acids (up to 10 mg/g DW). Thus, the obtained results showed significant differences in the qualitative and quantitative composition of metabolites between R. japonica and R. sachalinensis plants. Additionally, in this work, a cell culture of R. japonica was obtained and tested for its ability to synthesize and accumulate stilbenes.

A novel nonsense RPS26 mutation in a patient with Diamond–Blackfan anemia: a case report

BackgroundDiamond–Blackfan anemia is a rare congenital disorder characterized by erythroid hypoplasia and is associated with mutations in ribosomal protein genes. This case report describes a novel variant in the RPS26 gene, which, to our knowledge, has not been previously documented. Reporting this case adds to the understanding of Diamond–Blackfan anemia’s genetic diversity and phenotypic manifestations.Case presentationA 16-month-old Turkish girl presented with pallor and macrocytosis. There was no familial history of anemia. Hemoglobin electrophoresis showed hemoglobin F at 10.8%, hemoglobin A2 at 1.7%, and hemoglobin A at 87.5% (normal range 0–2%). Peripheral smear demonstrated macrocytosis and reticulocytopenia. Bone marrow examination revealed marked erythroid hypoplasia and dyserythropoiesis. Targeted next-generation sequencing, which included genes such as RPL11, RPL15, RPL26, RPL35A, RPL5, RPS10, RPS17, RPS19, RPS24, RPS26, RPS28, RPS29, RPS7, and TSR2, identified a heterozygous c.221G>T (p.C74F) variant in the RPS26 gene. This variant is reported here for the first time.ConclusionsThe identification of the c.221G>T (p.C74F) variant in RPS26 provides new insights into the genetic underpinnings of Diamond–Blackfan anemia. This finding underscores the importance of genetic testing in diagnosing Diamond–Blackfan anemia and highlights the potential for new mutations to contribute to the clinical presentation of the disease. Further research into RPS26 mutations may enhance the understanding of Diamond–Blackfan anemia’s pathogenesis and lead to improved diagnostic and therapeutic strategies.

Resistance gene enrichment sequencing for NLR genes for Phytophthora sojae in selected soybean plant introductions and differentials with putative novel and known Rps genes

AbstractNumerous sources of putative novel resistance genes toward Phytophthora sojae (Rps genes) have been identified and loci mapped in soybean (Glycine max L. Merr.) but cloning has remained elusive. We utilized resistance gene enrichment sequencing (RenSeq) to identify the putative resistance genes in 20 plant introductions (PIs) and differentials of the cultivar Williams with rps, Rps1c, Rps3a, and Rps8. The DNA from these genotypes was enriched and sequenced using more than 25,000 80 nt baits designed to nucleotide‐binding leucine‐rich repeat (NLR) encoding sequences. Overall, there were greater numbers of variants in the NLR‐encoding genes in Rps loci on chromosomes (Chrs) 3, 7, 13, and 18 for the 20 PIs as compared to the Williams differentials for rps, Rps1c, Rps1k, Rps3a, and Rps8. Genes encoding Rps1c, Rps3a, and Rps8 were proposed based on sequence differences among the differentials. Among the 20 PIs, there may be additional alleles on Chrs 3, 13, and 18, and PI399079 may have two new alleles at Chrs 3 and 7 loci. A unique NLR on Chr 8 was identified in PI200553. New alleles were also identified on Chrs 3 and 18 when the PI and resistant bulks were compared to susceptible recombinant inbred lines. This study demonstrates the utility of RenSeq as an efficient method to identify and predict specific novel NLR genes in landrace soybean germplasm, which confer resistance to P. sojae and obtain gene‐specific markers to facilitate their introgression into modern cultivars.

Genetic characteristics of the diploid offsprings in potato Cooperation 88 induced by diploid donor IVP101.

Diploid lines (2n = 2x = 24) derived from tetraploid potato cultivars have been utilized to hybridize with wild diploid potato species, yielding fertile offsprings. Utilizing the pollen of Solanum tuberosum Group Phureja, such as IVP101, IVP35 and IVP48, as an inducer for wide hybridization with tetraploid cultivars represents a common method for producing diploids. In this study, we created a distant hybridization induced population of tetraploid potato cultivar Cooperation 88 (C88) and IVP101, and screened all diploids using flow cytometry and ploidyNGS. We investigated the genetic composition of chloroplast and nuclear genomes in 43 diploid offsprings. We found that all diploid offsprings share the same chloroplast genomic sequence as C88 and no evidence of paternal chloroplast inheritance was found. Used SNP data to calculate the theoretical introgression index of IVP101 with diploid offsprings. The results showed that the inducer's nuclear genome was involved in the nuclear genome of the diploid offsprings with purple stem trait, indicating that the inducer nuclear genome was not completely eliminated in the nuclear genome during distant hybridization. Furthermore, we conducted a comparative analysis of the chloroplast genomes of the Solanum genus. The results indicated that (1) the chloroplast genome sizes of the 14 Solanum species ranged from 154,289 bp to 155,614 bp, with a total number of genes ranging 128-141, and with ycf1 and rps19 pseudogenes appearing at the IRB/SSC and IRA/LSC boundaries, respectively; (2) eight divergent hotspots distributed in the LSC and SSC regions of the Solanum chloroplast genomes were identified; (3) positive selection was detected in the clpP, rbcL, rps15, and rps4 genes, likely contributing to the adaptation of Solanum species to different habitats. These results reveal the variation and evolutionary characteristics of chloroplast genomes in Solanum plants.

Genetic dissection of resistance to Phytophthora sojae using genome-wide association and linkage analysis in soybean [Glycine max (L.) Merr.

Two novel and one known genomic regions associated with R-gene resistance to Phytophthora sojae were identified by genome-wide association analysis and linkage analysis in soybean. Phytophthora root and stem rot (PRR) caused by Phytophthora sojae is a severe disease that causes substantial economic losses in soybean [Glycine max (L.) Merr.]. The primary approach for successful disease management of PRR is using R-gene-mediated resistance. Based on the phenotypic evaluation of 376 cultivated soybean accessions for the R-gene type resistance to P. sojae (isolate 2457), a genome-wide association analysis identified two regions on chromosomes 3 and 8. The most significant genomic region (20.7-21.3 Mbp) on chromosome 8 was a novel resistance locus where no Rps gene was previously reported. Instead, multiple copies of the UDP-glycosyltransferase superfamily protein-coding gene, associated with disease resistance, were annotated in this new locus. Another genomic region on chromosome 3 was a well-known Rps cluster. Using the Daepung × Ilpumgeomjeong RIL population, a linkage analysis confirmed these two resistance loci and identified a resistance locus on chromosome 2. A unique feature of the resistance in Ilpumgeomjeong was discovered when phenotypic distribution was projected upon eight groups of RILs carrying different combinations of resistance alleles for the three loci. Interestingly, the seven groups carrying at least one resistance allele statistically differed from the other with none, regardless of the number of resistance alleles. This suggests that the respective three different resistance genes can confer resistance to P. sojae isolate 2457. Deployment of the three regions via marker-assisted selection will facilitate effectively improving resistance to particular P. sojae isolates in soybean breeding programs.

Tumor-suppressive activities for pogo transposable element derived with KRAB domain via ribosome biogenesis restriction

Transposable elements (TEs) are indispensable for human development, with critical functions in pluripotency and embryogenesis. TE sequences also contribute to human pathologies, especially cancer, with documented activities as cis/trans transcriptional regulators, as sources of non-coding RNAs, and as mutagens that disrupt tumor suppressors. Despite this knowledge, little is known regarding the involvement of TE-derived genes (TEGs) in tumor pathogenesis. Here, systematic analyses of TEG expression across human cancer reveal a prominent role for pogo TE derived with KRAB domain (POGK). We show that POGK acts as a tumor suppressor in triple-negative breast cancer (TNBC) cells and that it couples with the co-repressor TRIM28 to directly block the transcription of ribosomal genes RPS16 and RPS29, in turn causing widespread inhibition of ribosomal biogenesis. We report that POGK undergoes deactivation by isoform switching in clinical TNBC, altogether revealing its exapted activities in tumor growth control.

Chloroplast genome sequencing and divergence analysis of 18 Pyrus species: insights into intron length polymorphisms and evolutionary processes.

Pears constitute an essential temperate crop and are primarily produced through interspecific hybridization owing to self-incompatibility that complicates their breeding history. To address this, we sequenced the complete chloroplast (cp) genomes of 18 Pyrus and one Malus species using the Illumina HiSeq4000 platform. The cp genomes ranged from 159,885 bp to 160,153bp and exhibited a conserved circular DNA structure with an average GC content of 36.5%. Each cp genome contained 127 genes, including 83 protein-coding, 36 tRNA, and 8 rRNA genes. Divergence analysis with mVISTA showed high conservation in the coding regions and notable variations in the non-coding regions. All species shared 17 intron-containing genes, with ycf3 and clpP each having two introns. Five intron-containing genes (ndhB, rpl2, rps12, trnA-UGC, and trnE-UUC) were located in the inverted repeat regions, while trnL-UAA was located in the large single-copy region, with conserved intron lengths across Pomoideae. We identified polymorphic intron sequences in the rpl22, petB, clpP, ndhA, and rps16 genes and designed primers for these regions. Notably, the two Pyrus ussuriensis accessions Doonggeullebae and Cheongdangrori showed intron-length polymorphisms despite being classified as the same species. Phylogenetic analysis of the cp genome sequences revealed two major clusters, indicating distinct maternal lineages and evolutionary origins. This study underscores the importance of cp gene polymorphisms in P. fauriei, P. calleryana, P. ussuriensis, and P. pyrifolia, providing valuable insights into Pyrus evolution as well as aiding in the conservation and breeding of pear germplasm.

From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation

BackgroundPlastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy and carbon dioxide, converting them into chemical energy and oxygen, which are crucial for plant development and adaptation. However, little is known about the plastid genome to light adaptation. Petrocosmea, a member of the Gesneriaceae family, comprises approximately 70 species with diverse light environment, serve as an ideal subject for studying plastomes adapt to light.ResultsIn this study, we selected ten representative species of Petrocosmea from diverse light environments, assembled their plastid genomes, and conducted a comparative genomic analysis. We found that the plastid genome of Petrocosmea is highly conserved in both structure and gene content. The phylogenetic relationships reconstructed based on the plastid genes were divided into five clades, which is consistent with the results of previous studies. The vast majority of plastid protein-coding genes were under purifying selection, with only the rps8 and rps16 genes identified under positive selection in different light environments. Notably, significant differences of evolutionary rate were observed in NADH dehydrogenase, ATPase ribosome, and RNA polymerase between Clade A and the other clades. Additionally, we identified ycf1 and several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, and trnS-trnG) as candidate barcodes for this emerging ornamental horticulture.ConclusionWe newly assembled ten plastid genomes of Petrocosmea and identified several hypervariable regions, providing genetic resources and candidate markers for this promising emerging ornamental horticulture. Furthermore, our study suggested that rps8 and rps16 were under positive selection and that the evolutionary patterns of NADH dehydrogenase, ATPase ribosome, and RNA polymerase were related to the diversity light environment in Petrocosmea. This revealed an evolutionary scenario for light adaptation of the plastid genome in plants.

Light signaling-dependent regulation of plastid RNA processing in Arabidopsis.

Light is a vital environmental signal that regulates the expression of plastid genes. Plastids are crucial organelles that respond to light, but the effects of light on plastid RNA processing following transcription remain unclear. In this study, we systematically examined the influence of light exposure on plastid RNA processing, focusing on RNA splicing and RNA editing. We demonstrated that light promotes the splicing of transcripts from the plastid genes rps12, ndhA, atpF, petB, and rpl2. Additionally, light increased the editing rate of the accD transcript at nucleotide 794 (accD-794) and the ndhF transcript at nucleotide 290 (ndhF-290), while decreasing the editing rate of the clpP transcript at nucleotide 559 (clpP-559). We have identified key regulators of signaling pathways, such as CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1), ELONGATED HYPOCOTYL 5 (HY5), and PHYTOCHROME-INTERACTING FACTORs (PIFs), as important players in the regulation of plastid RNA splicing and editing. Notably, COP1 was required for GENOMES UNCOUPLED1 (GUN1)-dependent repression of clpP-559 editing in the light. We showed that HY5 and PIF1 bind to the promoters of nuclear genes encoding plastid-localized RNA processing factors in a light-dependent manner. This study provides insight into the mechanisms underlying light-mediated post-transcriptional regulation of plastid gene expression.

Evolving Archetypes: Learning from Pathogen Emergence on a Nonmodel Host.

Research initiatives undertaken in response to disease outbreaks accelerate our understanding of microbial evolution, mechanisms of virulence and resistance, and plant-pathogen coevolutionary interactions. The emergence and global spread of Pseudomonas syringae pv. actinidiae (Psa) on kiwifruit (Actinidia chinensis) showed that there are parallel paths to host adaptation and antimicrobial resistance evolution, accelerated by the movement of mobile elements. Significant progress has been made in identifying type 3 effectors required for virulence and recognition in A. chinensis and Actinidia arguta, broadening our understanding of how host-mediated selection shapes virulence. The rapid development of Actinidia genomics after the Psa3 pandemic began has also generated new insight into molecular mechanisms of immunity and resistance gene evolution in this recently domesticated, nonmodel host. These findings include the presence of close homologs of known resistance genes RPM1 and RPS2 as well as the novel expansion of CCG10-NLRs (nucleotide-binding leucine-rich repeats) in Actinidia spp. The advances and approaches developed during the pandemic response can be applied to new pathosystems and new outbreak events.

The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata.

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.

Genome-Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi-Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves.

Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point,and so forth. Furthermore, we combined genome-wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS-type) and Maker00003187 (P-type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1,and rpoC2 in our previous studyand the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNApull-down assays revealed that Maker00002998 PPR protein might be involved in the post-transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.

Genotypes analysis and antifungal susceptibility of Candida albicans strains isolated from women with vaginal candidiasis in Jordan using PCR targeting 25SrDNA and ALT repeat sequences of the RPS.

Genotypic identification of the etiologic agents of vaginal candidiasis (VC) is of significance in epidemiologic studies and in the establishment of adequate treatment protocol. The aim of this study was to determine the antifungal susceptibility and gene diversity of C. albicans isolated from a group of Jordanian women with VC. A total of 312 isolates of candida species, recovered from women with vaginal candidiasis who attended gynecology clinics affiliated to three major private hospitals in Amman over a period of five months (July 2020 to December 2020) were included in this study. The isolated Candida were characterized by phenotypic and genotypic means. Genotypic studies were performed using specific PCR primers of the rDNA and RPS genes. Susceptibility testing of all C. albicans isolates was conducted following the National Committee for Clinical Laboratory Standards and E-test strips. Candida albicans was the most dominant Candida spp. that caused VC among the studied population. C. albicans isolates were found to be of three different subtypes at the 25S rDNA gene. All isolates belonged to genotypes A, B and C while genotypes D and E were not detected. The diversity of C. albicans was higher on the basis of RPS region where the use of two markers (P-I and P-II) resulted in the identification of nine distinct C. albicans subtypes. The sensitivity testing revealed variations in the susceptibility of various genotypes to different antifungal drugs. Genotype A isolates were more susceptible to fluconazole, flucytosine and ketoconazole than genotypes B and C. Candida albicans incriminated as etiologic agents of vaginitis among Jordanian women exhibited relationship between various genotypes and antifungal drugs.