Repeat Region Research Articles

The complete chloroplast genome sequence of Cathetus clarkei Hook.f.1890 R.W.Bouman, 2022 (Phyllanthaceae)

Cathetus clarkei, a significant folk medicinal plant, is utilized to treat a variety of ailments. In this study, we reported the complete chloroplast genome sequence of this species. The length of the complete chloroplast genome was 155,810 bp, included a pair of inverted repeat (IR) regions (26,340 bp), a large single-copy region (LSC, 84,853 bp), and a small single-copy region (SSC, 18,277 bp). It comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The total GC content was 36.8%. The phylogenetic tree revealed that C. clarkei had a close relationship with P. cochinchinensis, followed by P. reticulatus. This study provides a reference for important medicinal plants within the Phyllanthaceae, and we can gain a deeper understanding of how the species adapts to changes in the environment, helping us to identify and protect it.

The complete chloroplast genome of Heracleum hemsleyanum Diels (Apioideae), a traditional medicinal herb in China

Heracleum hemsleyanum Diels is a traditional medicinal herb in China. We reported its first complete chloroplast genome. The chloroplast genome was 146,775 bp in length with 37.53% GC content, containing a large single copy region (LSC, 93,309 bp), a small single copy region (SSC, 17,502 bp), and a pair of inverted repeat regions (IRs, 17,982 bp). Moreover, the chloroplast genome encoded 130 genes, including 86 protein-coding genes (PCGs), 36 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Phylogenetic analysis indicated that H. hemsleyanum was closely related to Heracleum moellendorffii and Heracleum yungningense. This assembled chloroplast genome will provide vital information on the genetic resources, phylogenetic relationships, and the species identification of the genus Heracleum.

Elucidation of Postfusion Structures of the Measles Virus F Protein for the Structure-Based Design of Fusion Inhibitors.

Measles is a highly infectious disease and remains a major cause of childhood mortality worldwide. In some cases, the measles virus (MV) induces subacute sclerosing panencephalitis within several years of the acute infection. The infection of the target cells by MV is mediated by the F protein, in which two heptad repeat regions, HR1 and HR2, form a six-helix bundle before membrane fusion. We previously reported anti-MV peptides, which were designed from the HR region of the MV F protein. Here, we characterized the essential interactions between the HR1 and HR2 regions on the postfusion six-helix bundles of synthetic HR1 and HR2 peptides by crystallographic studies. Based on the crystal structures, we identified the minimal α-helix sequence for antiviral activity. Additionally, optimizing HR2 peptides by introducing α-helix-inducible motifs and maintaining key hydrogen bond networks at the N- and C-terminal regions led to the identification of highly potent antiviral peptides.

The complete chloroplast genome sequences of monotypic genus Pseudogalium, and comparative analyses with its relative genera

BackgroundPseudogalium is a new monotypic genus with two subspecies in China and one in Japan, which holds a distinctive phylogenetic position and ecological significance within the tribe Rubieae. Chloroplast genomes contain abundant information for resolving phylogenetic relationships. To investigate the phylogenetics of P. paradoxum and its related genera, we first sequenced, assembled, and annotated the chloroplast genome of two subspecies of P. paradoxum in China and reconstructed the phylogenetic trees. Due to the lack of samples of P. paradoxum subsp. franchetianum from Japan, this study only analyzed and discussed P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei.ResultsThis study had shown that the complete chloroplast genomes of Pseudogalium ranged from 153,093 bp to 153,333 bp in length with 130 genes in total, all of which had typical circular structures consisting of a large single-copy region, a small single-copy region and a pair of inverted repeat regions. The comparative analysis showed that the chloroplast genome of P. paradoxum was conserved in the inverted repeat regions. Additionally, we identified 60 dispersed repeat sequences, 61–63 simple sequence repeats, and 30 codons within the 82 protein-coding genes that exhibited RSCU values greater than one. Furthermore, we detected highly divergent regions that hold potential as new DNA barcodes for species identification. Compared with Pseudogalium, the gene number, gene length, and GC content in the chloroplast genomes of Galium and Rubia exhibited differential characteristics, and the dispersed repeat sequences and SSRs in Galium and Rubia were significantly different. Phylogenetic analysis based on the whole chloroplast genomes showed that Pseudogalium can be treated as a new genus, with P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei considered as two distinct subspecies of P. paradoxum.ConclusionsThe complete chloroplast genomes of P. paradoxum were first reported in this study, which provided a new insight into phylogeny and taxonomy of this genus. Phylogenetic analyses strongly supported the following proposals: (1) P. paradoxum can be isolated as a genus closely related to Galium; (2) P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei form distinct clades, both of which can be considered as subspecies of P. paradoxum.

The complete chloroplast genome of Barringtonia asiatica (L.) Kurz (Lecythidaceae)

Genomic resources for Barringtonia asiatica (L.) Kurz, a pantropical beach forest species native to the Philippines, have not been published to date, despite its medicinal importance and potential for biomedical applications. In this study, we assembled and characterized the first complete chloroplast genome of B. asiatica using Illumina paired-end sequencing technology. It displayed a typical quadripartite structure with a sequence length of 158,794 bp, comprised of a large single copy of 88,196 bp, small single-copy of 18,448 bp, and a pair of inverted repeat regions of 26,075 bp each. The cp genome contained 35 tRNA genes, eight rRNA genes, and 86 protein-coding genes with an overall GC content of 36.8%. Phylogenetic analysis revealed a close evolutionary relationship between B. racemosa and B. fusicarpa, forming a monophyletic group with B. asiatica with high bootstrap support, thereby enhancing our understanding of the phylogeny, systematics, and genetics of Asian Lecythidaceae species.

P-492. Quantification of HIV Shedding in Viremic Patients

Abstract Background Identifying pockets of undiagnosed HIV is a critical step in the U.S. Ending the HIV Epidemic (EHE). Wastewater-based epidemiology represents a novel way to build agnostic population-level data about disease distribution. We detected HIV virus in two sewersheds in Northern California. We are now conducting a study to measure how much HIV virus is shed into urine and stool, to better estimate cases represented by wastewater detection. HIV-1 RNA Detected in Concentrated Urine Methods We are recruiting participants from HIV clinics in San Mateo and Santa Clara Counties. Patients must be 18 years or older with HIV-1 viral load of >10,000 copies/ml at the time of recruitment. Subjects are asked to provide 5 weekly self-collected blood (Tasso), urine, and stool samples. The plasma is analyzed by established HIV-1 RNA quantitative PCR techniques. Nucleic acids from urine, concentrated (centrifuged) urine, and stool are suspended in DNA/RNA Shield, then extracted using the ZymoBIOMICS DNA/RNA Miniprep Kit (ZymoBIOMICS #R2002). HIV genome-specific primers target the Long Terminal Repeat (LTR) region of the HIV-1 genome. Droplets for digital droplet PCR are generated using the AutoDG Automated Droplet Generator. Reverse transcriptase PCR, which quantifies RNA and DNA combined, and direct PCR, which quantifies DNA, is then carried out with the Mastercycler Pro. Thresholding is performed using QX Manager Software. HIV-1 RNA Detected in Stool Results Two patients have been enrolled to date. Patient 1 was started on antiretroviral therapy after the first sample was obtained; Patient 2 was started on antiretroviral therapy 10 days before the first sample was collected. HIV-1 RNA was found in 87.5% (7/8) of concentrated urine samples, including 85.7% (6/7) of samples obtained while on ART (Table 1). Among stool samples, 25.0% (2/8) yielded HIV RNA, but only 14.3% (1/7) of those obtained on ART (Table 2). Nucleic acids were not detected in unconcentrated urine. Plasma viral load testing is pending, so only the initial clinical HIV-1 viral loads at enrollment are shown. Conclusion HIV-1 RNA is present in concentrated urine but also in stool samples of viremic patients, even up to five weeks after initiation of ART. When the study is complete, our results will bolster how to interpret HIV-1 detected in wastewater. Disclosures All Authors: No reported disclosures

The complete chloroplast genome and phylogenetic analysis of Persicaria jucunda (Meisn.) Migo (Polygonaceae)

Persicaria jucunda is a plant distributed at meadow or wetland. Our study reports the complete chloroplast genome. The chloroplast genome of P. jucunda is a typical tetrameric structure with a total length of 159,843 bp, containing a large single-copy (LSC) region of 84,350 bp, a small single-copy (SSC) region of 13,151 bp, and two inverted repeat regions (IRs) of 31,171 bp. The total GC content was 38.2%, 36.5% for the LSC region, 33.2% for the SSC region, and 41.5% for the IR region. The P. jucunda chloroplast genome contains 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 36 chloroplast genomes showed similarity to P. foliosa and P. kawagoeana among the species analyzed. The chloroplast genome provides a valuable genetic resource for phylogenetic studies.

Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from Magallana gigas infected tissues.

Since the 1990s, the Pacific oyster Magallana gigas has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole-genome analysis. Identification of the best method for extraction of high molecular weight (HMW) DNA and development of accurate bioinformatic pipelines for its characterization are now required. To this end, we evaluated and compared six HMW methods and one conventional DNA extraction kit for their ability to extract OsHV-1 DNA from M. gigas-infected tissues. We then evaluated the ability of ONT sequencing to produce an accurate OsHV-1 genome from both whole-genome and "adaptive sampling" (AS) sequencing approaches. Finally, we evaluated the efficiency of bioinformatics tools for de novo assembly and consensus calling to generate accurate OsHV-1 genomes. The HMW DNA extraction kit coupled with ONT sequencing and dedicated bioinformatics tools allowed us to produce accurate OsHV-1 genomes compared to those assembled using Illumina technology. The AS approach allowed up to 60% enrichment for viral data, and the long reads generated by ONT allowed the characterization of OsHV-1 isomers. Together with its portability, this sequencing shows great promise as a diagnostic tool for the characterization of unculturable aquatic viruses directly from host tissues.IMPORTANCEMany aquatic viruses threaten commercially valuable species and cause significant economic losses during outbreaks. To improve our understanding of the origin, transmission patterns and spread of these viruses, additional genomic data are essential. However, genomic characterization of unculturable large DNA viruses is a major challenge. In the present study, we have successfully evaluated the ability of ONT sequencing and adaptive sequencing (AS) to sequence and assemble the complete OsHV-1 genome. Our results show that it is now possible to sequence the whole genome of large DNA viruses directly from infected host tissue, without the need for prior in vitro propagation or prior laboratory steps for virus enrichment.

Phenotypic Heterogeneity of ADTKD-MUC1 Diagnosed Using VNtyper, a Novel Genetic Technique.

Molecular diagnosis of autosomal dominant tubulointerstitial kidney disease (ADTKD) due to variants in the MUC1 gene has long been challenging since variants lie in a large Variable Number of Tandem Repeat (VNTR) region, making identification impossible using standard short read techniques. Previously, we addressed this diagnostic limitation by developing a computational pipeline, named VNtyper, for easier reliable detection of MUC1 VNTR pathogenic variants from short read sequences. This led to unexpected diagnoses of ADTKD-MUC1 among patients with kidney disease referred for genetic testing, which we report here. Cross-sectional observational study. 4,040 patients referred to Necker Enfants-Malades Hospital from 2017 to 2023 for genetic testing for (1) glomerular disease, (2) ciliopathy, (3) congenital anomalies of the kidneys and urinary tracts (CAKUT), (4) ADTKD, or (5) chronic kidney disease (CKD) of unknown origin, in whom MUC1 had not been previously tested by SNaPshot mini-sequencing. Clinical suspicion of ADTKD. ADTKD-MUC1 diagnosed using VNtyper. Data were collected from patients in whom ADTKD-MUC1 was newly diagnosed and patients in whom ADTKD was clinically suspected were compared to those in whom ADTKD was not. We identified 40 patients with MUC1 variants by VNtyper, including 33 new index patients and 7 relatives. Of the 33 index cases, 20 had been suspected of having ADTKD based on clinical features, and in the other 13, ADTKD had not been considered. In patients in whom ADTKD had not been considered clinically, the detection rate was 0.05% (1/1895) among patients with glomerular disease, 1.2% (4/329) among patients with ciliopathy, 0.09% (1/1099) among patients with CAKUT and 2.5% (7/285) among patients with CKD of unknown origin. In six patients, there was no family history of kidney disease, and we confirmed de novo presentation in two patients by segregation studies. Observational study and selected referral population (may not represent the prevalence or phenotypes in the general kidney disease population). With VNtyper, we were able to diagnose new cases of ADTKD-MUC1 in a large cohort of patients with various phenotypes. Some patients had atypical phenotypes due to a variant in another gene, and some had no family history of kidney disease, suggesting de novo disease which was confirmed in two patients.

Validation of a multiplexed immunoassay for immunological analysis of pre erythrocytic malaria vaccines

The primary immunological readout for clinical trials of R21/MatrixM™ malaria vaccine, is total IgG antibody specific to the central four amino acid NANP repeat region of the circumsporozoite protein. A multiplexed assay, which includes NANP, was developed and validated for four antigens representing components of the R21 immunogen. Initial assay optimisation included validation of the HBsAg international standard. Further validation performed in Oxford covered intra and inter-assay, and inter-operator variability, accuracy of QC and standard curve material, and included bridging to a singleplex NANP6 ELISA. The assay was shown to be robust and specific, with a broad dynamic range. We report a strong linear relationship between NANP6 IgG as measured by the singleplex ELISA and the multiplexed assay with rho values of 0.89 and 0.88 for two separate clinical trials (both p < 0.0005). This assay can be used to measure antibodies specific to the CSP NANP repeat region, CSP C-term region, full length R21 and HBsAg.

Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus swinhoei Hance 1866 from the family Rosaceae

Rubus swinhoei Hance is an important plant owing to its medicinal root and edible fruit, and extensively distributed in China. In this study, we reported the complete chloroplast genome of R. swinhoei. The chloroplast genome was 156,335 bp in size with the overall GC content of 37.15%, having a circular and quadripartite structure, which contained a large single-copy (LSC) and a small single-copy (SSC) regions of 85,897 bp and 18,858 bp separated by a pair of 25,790 bp inverted repeat (IR) regions. The complete chloroplast genome comprised 131 unique genes of which 86 and 37 were protein-coding genes and tRNA genes, respectively, and also eight rRNA genes. The phylogenetic analysis revealed that R. swinhoei was closely related to R. kawakamii. The genome information reported in this paper will be beneficial for further investigation on the evolution of this species.

MOLECULAR AND GENETIC CHARACTERISTICS OF EPSTEIN-BARR VIRUS ISOLATES IN ADULT PATIENTS WITH HIV INFECTION IN NIZHNY NOVGOROD REGION

Abstract Introduction. According to international studies, the Epstein-Barr virus (EBV) isolates from individuals infected with the human immunodeficiency virus (HIV) are characterized by specific molecular genetic features compared to immunocompetent individuals. In Russia, no studies have yet been conducted to assessing EBV molecular genetic diversity in HIV-patients. The aim of the study is to assess EBV molecular genetic diversity in adult HIV-patients in the Nizhny Novgorod region. Materials and methods. EBV isolates derived from blood leukocytes of 138 HIV-infected patients aged 20–69 years (HIV(+) group) and 68 HIV-uninfected sex- and age-matched (HIV(-) group) individuals were studied. For differential detection of EBV-1/EBV-2, there were used PCR variant with electrophoretic detection of amplification products in agarose gel. Nucleotide sequences of the C-terminal fragment LMP-1 gene were determined by Sanger sequencing. Phylogenetic analysis was performed using MEGA X software. Results. In the typical pattern of Nizhny Novgorod region EBV isolates in the adults HIV(-) group, only EBV-1 was detected. In the HIV(+) group detection rate of EBV-1 was 88.2±3.4%, EBV-2 – 5.4±2.3%, EBV-1+VEB-2 – 6.4± 2.6% cases. In the EBV strain structure based on the classification by R. Edwards et al. five LMP-1 variants were identified: B95-8, China 1, Med-, NC and Alaskan, among which B95-8 was dominant. However, their frequency rate did not differ between the HIV(+) and HIV(-) groups. In general, in HIV infection, the appearance of recombinant EBV LMP-1 variants, a wider range of deletions, prominent variability in the tandem repeat region with the presence of modified motifs and point amino acid substitutions therein have been noted, and 57 amino acid substitutions have been described that were previously found in the Nizhny Novgorod region EBV isolates was not detected. Conclusion. For the first time in Russia, molecular genetic EBV diversity in adult HIV-patients was carried out. The results obtained build up the basis for a prospective study on a relationship between clinical and laboratory characteristics for EBV+HIV co-infection and genetic heterogeneity of EBV population at the level of virus types, variants and subvariants.

The complete chloroplast genome of Solanum melongena ‘Yunqie 9’

Solanum melongena ‘Yunqie 9’ was selected by the Horticultural Research Institute of Yunnan Academy of Agricultural Sciences based on the local environment of Yunnan Province. It is excellent in fruit quality and yield, but it is relatively weak in disease resistance. No information on complete chloroplast genome and position in the phylogeny of Solanum to restrict its genetic improvement. In this study, the chloroplast genome of ‘Yunqie 9’ was sequenced using Illumina high-throughput sequencing technology. The size of the complete chloroplast genome was 155,579 bp in length with an GC content of 37.70%, composed of a large single-copy region (86,189 bp), a small single-copy region (18,504 bp), and a pair of inverted repeat regions (25,443 bp). A total of 134 coding genes were annotated in the entire chloroplast genome, including 89 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis based on chloroplast genome sequences of 20 species in the Solanaceae family indicated that except for the cultivated Solanum, ’Yunqie 9’ was closely related to Solanum melongena×Solanum torvum and Solanum insanum.

R21 in Matrix-M adjuvant in UK malaria-naive adult men and non-pregnant women aged 18-45years: anopen-label, partially blinded, phase 1-2a controlled human malaria infection study.

R21 is a novel malaria vaccine, composed of a fusion protein of the malaria circumsporozoite protein and hepatitis Bsurface antigen. Following favourable safety and immunogenicity in a phase 1study, we aimed to assess the efficacy of R21 administered with Matrix-M (R21/MM) against clinical malaria in adults from the UK who were malaria naive in a controlled human malaria infection study. In this open-label, partially blinded, phase 1-2A controlled human malaria infection study undertaken inOxford, Southampton, and London, UK, we tested five novel vaccination regimens of R21/MM. Astandard three-dose regimen (groups 1and 6) was compared with a reduced (fractional) third dose (groups 2and 5) of R21/MM, concomitant administration with viral vectors ChAd63-MVA expressing ME-TRAP (group 3), and a two-dose R21/MM regimen (group 7). Controlled Human Malaria Infection (CHMI) was delivered by mosquito bite at Imperial College London, London, UK, 3-4 weeks after final vaccination (or 18months after final vaccination for group 6) alongside unvaccinated controls (groups 4A and 4B). The primary outcome measures were to assess safety of the vaccines in healthy malaria-naive volunteers and the efficacy (occurrence of blood-stage malaria infection) of the different vaccine regimens compared with non-vaccinated controls after CHMI. The trial was registered with ClinicalTrials.gov (NCT02905019). 66volunteers were enrolled with 59undergoing subsequent CHMI. All vaccination schedules were well tolerated. The highest level of protection against CHMI was observed in participants receiving the standard three-dose regimen of R21/MM (group 1, nine of 11volunteers protected) with protection maintained in three of five volunteers re-challenged by CHMI 7·5months later. Protection against malaria was also seen in group 2, group 3, and group 5compared with unvaccinated control participants. Total IgG antibody responses to the NANP repeat region of circumsporozoite protein peaked after the third dose of R21/MM in all volunteers and were well maintained to 90days after challenge. Reducing the third dose did not affect protection or antibody concentrations. Our study shows that R21/MM elicits high-level efficacy against clinical malaria in a controlled human infection model of malaria in adults who are malaria naive. These data supported the evaluation of R21/MM in field efficacy trials in the target population of young children in malaria-endemic areas. EU Horizon 2020, the UK Medical Research Council, the European Commission, the UK National Institute of Health Research, the Imperial NIHR Clinical Research Facility, the Oxford NIHR Biomedical Research Centre, and the Wellcome Trust.

Comparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships of 21 Sect. Camellia (Camellia L.) Plants.

Background: Section Camellia is the most diverse group in the genus Camellia L., and this group of plants has a long history of cultivation in China as popular ornamental flowers and oil plants. Sect. Camellia plants present diverse morphological variations and complexity among species, resulting in uncertainty in the classification of species, which has resulted in a degree of inconvenience and confusion in the use of plant resources and research. Methods: Here, We sequenced and assembled the chloroplast genomes of 6 sect. Camellia and performed comparative chloroplast genome analysis and phylogenetic studies combined with 15 existing sect. Camellia plants. Results: The chloroplast genome of 21 species in sect. Camellia species were quadripartite with length of 156,587-157,068 bp base pairs (bp), and a highly conserved and moderately differentiated chloroplast genome arrangement. The 21 sect. Camellia chloroplast genomes were similar to those of angiosperms, with high consistency in gene number, gene content and gene structure. After the annotation process, we identified a total of 132 genes, specifically 87 sequences coding for proteins (CDS), 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The ycf1 gene in 21 species of the sect. Camellia was present only in the small single-copy/inverted repeat of a (SSC/IRa) region. Sequence variation was greater in the large single-copy (LSC) region than in the IR region, and the majority of the protein-coding genes presented high codon preferences. The chloroplast genomes of 21 plant species exhibit relatively conserved SC (single copy region)/IR (inverted repeat region) boundaries. We detected a total of 2975 single sequence repeats (SSRs) as well as 833 dispersed nuclear elements (INEs). Among these SSRs, A/T repeats and AT/AT repeats dominated, while among INEs, forward repeats and palindromic repeats predominated. Codon usage frequencies were largely similar, with 30 high-frequency codons detected. Comparative analysis revealed five hotspot regions (rps16, psaJ, rpl33, rps8, and rpl16) and two gene intervals (atpH-atpI and petD-rpoA) in the cp genome, which can be used as potential molecular markers. In addition, the phylogenetic tree constructed from the chloroplast genome revealed that these 21 species and Camellia oleifera aggregated into a single branch, which was further subdivided into two evolutionarily independent sub-branches. Conclusions: It was confirmed that sect. Camellia and C. oleifera Abel are closely related in Camellia genus. These findings will enhance our knowledge of the sect. Camellia of plants, deepen our understanding of their genetic characteristics and phylogenetic pathways, and provide strong support for the scientific development and rational utilization of the plant resources of the sect. Camellia.

The complete chloroplast genome of Hemisteptia lyrata (Bunge) Fisch. & C. A. Mey. 1836 (Asteraceae) and its phylogenetic analysis

Hemisteptia lyrata, widely distributed in China, has a 152,467 bp chloroplast genome with a large single-copy (LSC) region of 83,473 bp, a small single-copy (SSC) region of 18,594 bp, a pair of inverted repeat regions (IRs) of 25,194 bp in length. The GC content is 36.46%. A total of 133 genes were encoded, of which 88 were protein coding genes, eight were rRNA genes, and 37 were tRNAs. The phylogenetic analysis using the maximum-likelihood method showed that H. lyrata is closely related to the species in Saussurea. This study provides genomic resources for phylogenetic genetics and resource exploitation of H. lyrata.

The Complete Chloroplast Genome of Erythrina variegata L. (Papilionoideae, Fabaceae).

Erythrina variegata L. 1754, a thorny deciduous tree of Fabaceae, contains various chemical compounds such as alkaloids, flavonoids, and triterpenoids and exhibits anti-depressant, anti-inflammatory, and antidiabetic activities. However, genomic data of E. variegata are limited. In this study, the complete chloroplast genome of E. variegata was sequenced and characterized using Illumina sequencing platform. The chloroplast genome of E. variegata was 152,351 bp in length and consisted of a large single copy (82,907 bp), a small single copy (26,309 bp), and two inverted repeat regions (16,826 bp). There were 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Comparative analysis revealed high conservation of chloroplast genomes among Erythrina species regarding genome size, structure, and gene content. The phylogenetic study also indicated a close relationship between E. variagata and E. sanwicensis. This study provides initial plastome data for further genomic studies examining E. variegata and related species in Fabaceae.

Complete chloroplast genomes of Lespedeza inschanica and L. juncea (Fabaceae: section Junceae)

Species of the section Junceae (Lespedeza, Fabaceae) have been used in traditional medicine, and their extracts have been investigated as medicinal resources in Korea. However, their morphological similarities may lead to misidentification and misuse. In this study, we analyzed the chloroplast genomes of Lespedeza inschanica and Lespedeza juncea to obtain more evidence to assist with the classification of this section. Both genomes are approximately 149 kb long, comprising large single-copy, small single-copy, and inverted repeat regions, with a total of 128 genes. The genomes in Lespedeza exhibit shared features, including the loss of infA and rpl22 genes, the loss of rpl2 and rps12 introns, and inversion of the trnD-Y-E cluster. A phylogenetic analysis supported Junceae as a monophyletic section that includes two clades. One clade comprised Lespedeza cuneata, L. inschanica, and L. juncea, whereas the other includes Lespedeza davurica and Lespedeza floribunda. This study provides foundational data pertaining to the taxonomy of Lespedeza.

Complete chloroplast genome of Syzygium glomeratum (Myrtaceae) and phylogenetic analysis

Syzygium glomeratum (Lam.) DC., known as “Tram Tron” in Vietnam, is an evergreen tree known for its medicinal properties. To understand the genomic and evolutionary basis of this plant, we sequenced and assembled the complete chloroplast genome of S. glomeratum for the first time, using the Illumina platform. The complete chloroplast of S. glomeratum was 158,469 bp in length and contained a large single-copy region (87,962 bp) and a small single-copy region (18,391 bp) separated by inverted repeat regions (26,058 bp). The genome encoded 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A phylogenetic analysis of 42 Syzygium species revealed significant insight into their evolutionary relationships, indicating a closer relationship between S. glomeratum and its sister group (S. cinereum and S. claviflorum). In conclusion, our results provide genomic information pertaining to the chloroplast genome in S. glomeratum, which is also genetic information useful for further study of biodiversity, conservation, and evolutionary biology.

Elucidation of intragenomic variation of ribosomal DNA sequences in the enigmatic fungal genus Ceraceosorus, including a newly described species Ceraceosorus americanus

AbstractMulticopy nuclear ribosomal DNA (rDNA) genes have been used as markers for fungal identification for three decades. The rDNA sequences in a genome are thought to be homogeneous due to concerted evolution. However, intragenomic variation of rDNA sequences has recently been observed in many fungi, which may make fungal identification and species abundance estimation based on these loci problematic. Ceraceosorus is an enigmatic genus in the smut lineage Ustilaginomycotina for which very limited distribution data exist. Our previous research demonstrated intragenomic variation in the internal transcribed spacer (ITS1-5.8S-ITS2) region of two Ceraceosorus species. In this study, we described the fourth known species of Ceraceosorus, C. americanus, isolated from an asymptomatic rosemary leaf collected in Louisiana, USA. This is the first report of this genus in the Americas. We then selected all four known Ceraceosorus species, plus exemplar smut fungi representing all major lineages of subphylum Ustilaginomycotina, to examine sequence heterogeneity in three regions of the rDNA repeat (partial 18S, ITS, and partial 28S regions). Three methods were used: PCR-cloning-Sanger sequencing, targeted amplicon high-throughput sequencing, and whole-genome shotgun high-throughput sequencing. Our results show that Ceraceosorus is the only sampled fungal genus in Ustilaginomycotina with significant intragenomic variation at the ITS, with up to 25 nucleotide variant sites in the ITS1–5.8S–ITS2 region and 2.6% divergence among analyzed ITS haplotypes. We found many conflicting patterns across the three detection methods, with up to 27 conflicting variant sites recorded from a single individual. At least 40% of the conflicting patterns are possibly due to PCR-cloning-sequencing errors, as the corresponding variant sites were not observed in the other detection methods. Based on our data and the literature, we evaluated the characteristics and advantages/disadvantages of each detection method. Finally, a model for how intragenomic variation in the rDNA copies within a genome may arise is presented.