Intrageneric structural variation in organelle genomes from the genus Dystaenia (Apiaceae): genome rearrangement and mitochondrion-to-plastid DNA transfer

IntroductionDuring plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed.MethodsIn this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome).Results and DiscussionWe identified the putative functional transfers of the mitochondrial genes 5′ rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineage-specific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome. This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae

Corrigendum: The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of the plant Ampelopsis.</p

Diagnosis and Prognosis Using Machine Learning Trained on Brain Morphometry and White Matter Connectomes

Accurate, reliable prediction of risk for Alzheimer’s disease (AD) is essential for early, diseasemodifying therapeutics. Multimodal MRI, such as structural and diffusion MRI, is likely to contain complementary information of neurodegenerative processes in AD. Here we tested the utility of commonly available multimodal MRI (T1-weighted structure and diffusion MRI), combined with high-throughput brain phenotyping—morphometry and connectomics—and machine learning, as a diagnostic tool for AD. We used, firstly, a clinical cohort at a dementia clinic (study 1: Ilsan Dementia Cohort; N=211; 110 AD, 64 mild cognitive impairment [MCI], and 37 subjective memory complaints [SMC]) to test and validate the diagnostic models; and, secondly, Alzheimer’s Disease Neuroimaging Initiative (ADNI)-2 (study 2) to test the generalizability of the approach and the prognostic models with longitudinal follow up data. Our machine learning models trained on the morphometric and connectome estimates (number of features=34,646) showed optimal classification accuracy (AD/SMC: 97% accuracy, MCI/SMC: 83% accuracy; AD/MCI: 97% accuracy) with iterative nested cross-validation in a single-site study, outperforming the benchmark model (FLAIR-based white matter hyperintensity volumes). In a generalizability study using ADNI-2, the combined connectome and morphometry model showed similar or superior accuracies (AD/HC: 96%; MCI/HC: 70%; AD/MCI: 75% accuracy) as CSF biomarker model (t-tau, p-tau, and Amyloid β, and ratios). We also predicted MCI to AD progression with 69% accuracy, compared with the 70% accuracy using CSF biomarker model. The optimal classification accuracy in a single-site dataset and the reproduced results in multisite dataset show the feasibility of the high-throughput imaging analysis of multimodal MRI and data-driven machine learning for predictive modeling in AD

Diversity of medicinal plants used as male contraceptives: An initiative towards herbal contraceptives

In the recent era, population control is a global issue as well as national community health concern. Plants are being used as a source of medicines by human beings since ancient time. This study highlights the collection, identification and diversity of medicinal plants concerning their traditional knowledge to get better access to the herbal male contraception. Local informants and traditional health practitioners were consulted for information about the local names, distribution, part used and mode of utilization of the medicinal plant. To select plants with high medicinal uses, different quantitative measurements i.e. Relative Frequency of Citation (RFC), Disease Consensus Index (DCI) and descriptive methods of Jaccard Index (JI) was performed. A total of 100 plant species (used for infertility by the local communities) belonging to 50 families and 91 genera were collected. Jaccard Index results showed that 28 plant species were reported for the first time used as male contraceptives in Pakistan. The frequency of citation (FC) value ranged from 35 to 56. Plants with high Relative frequency of citation (RFC) and Disease Consensus index (DCI) values showed a high consensus for the antifertility among informants and THPs. Our study is focused on the diversity and priority of medicinal plants as male contraceptives.

Towards a transnational aesthetics: Literary displacement and translation as a transnational narrative space

This dissertation explores the literary practices located at the intersection between the national and the transnational, discussing transnational narrative spaces as a type of writing that operates outside the national canon. In The Remains of the Day, the problematic narrative that Ishiguro creates can be analyzed in terms of Bakhtin\u27s notion of parodic stylization. Ishiguro reproduces complete images, languages, and ideological belief systems in Bakhtinian parodic stylization and leads the reader to a conclusion that displaces radically the point of view of the narrator. In The Pickup, Gordimer explores transnational identity within a global setting, gesturing toward some kind of transnational identity that dislocates any stable identity formation and signification system in the framework of the nation-state or Empire. Gordimer imagines and articulates such a revolutionary transformation, especially focusing on the issue of relocation. The in-between area of translation is interrogated as a space where transnational identity is formed both in Morrison\u27s Beloved and Lee\u27s Native Speaker. In Beloved, Morrison is specifically conscious of the representation of slaves by the Master\u27s language, and her literary attempt to examine the process of this problematic representation can be viewed in terms of a particular type of translation practice: a translation of a political, social, and cultural minority into the language of the majority. Chang-rae Lee\u27s Native Speaker does not narrate the production of a fully constituted national subject, but shifts in perspective from a nationally oriented narrative of immigration to a fragmented, transnational narrative. The particular construction of transnational identity that re-imagines a particular mode of crossing the Asian American identity is made and unmade through the metaphor of translator. All the novels embody in various literary forms the possible models for a transnational fiction whose agenda is mainly dissidence/negation and nomadic mobility. Such literary attempts for dissidence/negation should be regarded not in terms of a breakdown, but rather in terms of an opening-up of signification with a new permissiveness that affords the opportunity for alternative meanings and relationships

Complete chloroplast genome features and phylogenetic implications of Cardamine fallax (O. E. Schulz) Nakai

Cardamine fallax (O. E. Schulz) Nakai. is a perennial plant distributed in Eastern Asia. However, no extensive genomic studies are available on C. fallax. In this paper, the authors describe the complete chloroplast (cp) genome of C. fallax and its phylogenetic analysis. The cp genome is 154,797 bp in length with 36.3% GC content and consists of a pair of inverted repeats (IRs) of 26,521 bp that separated a large single-copy (LSC) region of 83,817 bp and a small single-copy (SSC) region of 17,938 bp. It was found to contain 113 unique genes, of which 80 were protein-coding genes, 29 were transfer RNAs, and four were ribosomal RNAs. Also, six PCGs, eight tRNA and four rRNA genes were duplicated in the IR region and one gene as a pseudogene. Phylogenetic analysis showed that all Cardamine species are highly conserved, and C. fallax was associated with the sister clade C. amaraeformis and C. parviflora

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of the plant Ampelopsis