An investigation on the chloroplast and nuclear genomes of taxa belong to the subgenus Dracunculus (Bess.) Rydb. of Artemisia L. (Asteraceae) in Turkey

Artemisia is one of the biggest genera in the family Asteraceae, with around 500-600 taxa at specific and sub-specific levels and organised in 5 subgenera. Due to the high number of taxa, a lot taxonomists are trying to solve the problem of its classification and phylogeny but its natural classification still hasn’t been achieved. In this research, 60 individuals belonging to 4 taxa of the subgenus Dracunculus of Artemisia L. in Turkey were examined. For all the examined individuals from both the same and different populations belonging to the taxa of the subgenus Dracunculus, the sequences of the regions both psbA-trnH of chloroplast DNA and ITS of nuclear DNA were determined. Also, the gene regions obtained were recorded in the NCBI GenBank database and an accession number was taken. It was found that there was no gene flow and hybridization between the four studied taxa of the subgenus Dracunculus, and these 4 taxa also completed their speciation. According to the results of this molecular study, A. campestris var. campestris, A. campestris var. marschalliana and A. campestris var. araratica were proposed to be raised from the variety level to the species level. This research is important as it is the first molecular based study relating with the subgenus Dracunculus growing in Turkey.

Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

Horizontal transfer of microbial toxin genes to gall midge genomes

A growing body of evidence has underscored the role of horizontal gene transfer (HGT) in animal evolution. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (cdtB) from the pea aphid Acyrthosiphon pisum secondary endosymbiont (APSE) phages to drosophilid and aphid nuclear genomes. Here, we report cdtB in the nuclear genome of the gall-forming ‘swede midge’ Contarinia nasturtii (Diptera: Cecidomyiidae) via HGT. We searched all available gall midge genome sequences for evidence of APSE-to-insect HGT events and found five toxin genes (aip56, cdtB, lysozyme, rhs, and sltxB) transferred horizontally to cecidomyiid nuclear genomes. Surprisingly, phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor lineage of the toxin gene to cecidomyiids. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for animal HGT, which suggested that microbe-to-insect HGT was more likely between taxa that share environments than those from different environments. Many of the toxins we found in midge genomes target eukaryotic cells, and catalytic residues important for toxin function are conserved in insect copies. This class of horizontally transferred, eukaryotic cell-targeting genes is potentially important in insect adaptation.

A Genetic Perspective on Cetacean Evolution

Studies of cetacean evolution using genetics and other biomolecules have come a long way—from the use of allozymes and short sequences of mitochondrial or nuclear DNA to the assembly of full nuclear genomes and characterization of proteins and lipids. Cetacean research has also advanced from using only contemporary samples to analyzing samples dating back thousands of years, and to retrieving data from indirect environmental sources, including water or sediments. Combined, these studies have profoundly deepened our understanding of the origin of cetaceans; their adaptation and speciation processes; and of the past population change, migration, and admixture events that gave rise to the diversity of cetaceans found today. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Next-generation sequencing is now utilized to identify genetic abnormalities and develop gene therapy

The genomic size, complexity, heritability, and diversity of human primary genetic compartments vary. Although the nuclear genome's huge size ensures that hundreds of reported monogenic diseases appear in a range of conditions, germline abnormalities in the mitochondrial and nuclear genomes often generate developmental issues. Accumulation of somatic mutations in the nuclear genome causes cancer, and somatic mutations in mitochondria may contribute to aging. More broadly, the microbial metagenome develops largely after birth, and is marked throughout their lifetimes by much more diversity and diversity among individuals. Mitochondrial sequencing, clinical exome and full-genome sequencing, and 16S and unbiased microbiological sequencing have all become more widely available because of developments in DNA sequencing next-generation.These technologies discover genetic defects that can be addressed with gene therapy. Modern aided techniques of reproduction, such as mitochondrial replacement therapy and preimplantation diagnosis, may address complete genomic compartments in bulk, such as mitochondrial and nuclear genomes. Additive somatic cell gene therapies started with the invention of viral vectors to infect human somatic cells that could be cultured ex vivo, such as T cells, and rapidly advanced to in vivo applications employing viral pseudotypes with specific tissue tropisms. CRISPR/Cas9 and other targeted gene editing approaches that fix the specific causative mutation or gene at its endogenous locus have recently expanded the possibility for more refined ex vivo and in vivo gene therapies.DNA sequencing costs have decreased during the past two decades, hurrying to identify genetic diseases. Targeted gene editing progress has now enabled the synthesis and testing of specific therapeutic reagents to address direct and accessible genetic abnormalities, repeating these diagnostic accomplishments. Generalized methods for delivering customizable gene editing reagents to the cell type and genomic compartment of interest in the specific genetic disease of a patient are one of the major outstanding challenges to wide-spread gene therapy. Aside from direct genetic disease repair, recent methods for rapidly identifying synthetic genetic circuits capable of improving cellular function in diseases such as cancer and autoimmune hold the promise of future gene therapy in modified somatic cells.Genetic diseases are becoming more readily diagnosed in all human genetic compartments, and the next generation of gene therapy platforms targeting each compartment are preparing to give flexible, tailored curative medicines. The Mitochondrial genome, nuclear genome, and microbial metagenome are the three genetic compartments present in humans. Gene therapies for each of these compartments come into three categories: whole genome replacement or selection, non-focused insertion of new genetic information to compensate for genetic errors, and direct gene editing to correct causative genetic disorders. The mitochondrial and nuclear genomes are determined at conception, save for somatic mutations and the adaptive immune receptor repertoire, and remain stable throughout life.

Genomic diversity of 39 samples of Pyropia species grown in Japan

Some Pyropia species, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples of Pyropia species grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and Chinese P. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and Chinese P. yezoensis. Analysis of organellar genomes showed that the genetic diversity of Japanese P. yezoensis used in this study is lower than that of Chinese wild P. yezoensis. To analyze the genetic relationships between samples of Japanese Pyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding between P. yezoensis and P. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of Japanese P. yezoensis is low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain of P. yezoensis showed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation of Pyropia species.