Ubiquity of the St chloroplast genome in St-containing Triticeae polyploids

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 846-852 ◽  
Author(s):  
Margaret G Redinbaugh ◽  
Thomas A Jones ◽  
Yiting Zhang
Keyword(s):  
Dna Sequences ◽  
Nuclear Genome ◽  
Neighbor Joining ◽  
Mode Of Reproduction ◽  
Grass Family ◽  
Triticeae Species ◽  
Interspecies Hybridization ◽  
Cytoplasmic Dna ◽  
Nuclear Genomes ◽  
Cpdna Inheritance

Interspecific hybridization occurs between Tritceae species in the grass family (Poaceae) giving rise to allopolyploid species. To examine bias in cytoplasmic DNA inheritance in these hybridizations, the sequence of the 3' end of the chloroplast ndhF gene was compared among 29 allopolyploid Triticeae species containing the St nuclear genome in combination with the H, I, Ns, P, W, Y, and Xm nuclear genomes. These ndhF sequences were also compared with those from diploid or allotetraploid Triticeae species having the H, I, Ns, P, W, St, and Xm genomes. The cpDNA sequences were highly similar among diploid, allotetraploid, allohexaploid, and allooctoploid Triticeae accessions containing the St nuclear genome, with 0-6-nucleotide (nt) substitutions (0-0.8%) occurring between pairs of species. Neighbor-joining analysis of the sequences showed that the ndhF DNA sequences from species containing the St nuclear genome formed a strongly supported clade. The data indicated a strong preference for cpDNA inheritance from the St nuclear genome-containing parent in hybridizations between Triticeae species. This preference was independent of the presence of the H, I, Ns, P, W, and Xm nuclear genomes, the geographic distribution of the species, and the mode of reproduction. The data suggests that hybridizations having the St-containing parent as the female may be more successful.Key words: interspecies hybridization, cytoplasmic inheritance.

Genetic Disease and Therapy

2021 ◽  
Vol 16 (1) ◽  
pp. 145-166
Author(s):  
Theodore L. Roth ◽  
Alexander Marson
Keyword(s):  
Dna Sequences ◽  
Current Practice ◽  
Genetic Diseases ◽  
Genetic Material ◽  
Nuclear Genome ◽  
Genetic Alterations ◽  
Genetic Diagnostics ◽  
Gene Therapies ◽  
Disease Risks ◽  
Diagnosis Therapy

Genetic diseases cause numerous complex and intractable pathologies. DNA sequences encoding each human's complexity and many disease risks are contained in the mitochondrial genome, nuclear genome, and microbial metagenome. Diagnosis of these diseases has unified around applications of next-generation DNA sequencing. However, translating specific genetic diagnoses into targeted genetic therapies remains a central goal. To date, genetic therapies have fallen into three broad categories: bulk replacement of affected genetic compartments with a new exogenous genome, nontargeted addition of exogenous genetic material to compensate for genetic errors, and most recently, direct correction of causative genetic alterations using gene editing. Generalized methods of diagnosis, therapy, and reagent delivery into each genetic compartment will accelerate the next generations of curative genetic therapies. We discuss the structure and variability of the mitochondrial, nuclear, and microbial metagenomic compartments, as well as the historical development and current practice of genetic diagnostics and gene therapies targeting each compartment.

scholarly journals Tracking the Distribution and Burst of Nuclear Mitochondrial DNA Sequences (NUMTs) in Fig Wasp Genomes

Insects ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 680
Author(s):  
Jian-Xia Wang ◽  
Jing Liu ◽  
Yun-Heng Miao ◽  
Da-Wei Huang ◽  
Jin-Hua Xiao
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Theoretical Basis ◽  
Nuclear Genome ◽  
Distribution Patterns ◽  
Good Evidence ◽  
Fig Wasp ◽  
Fig Wasps ◽  
Exogenous Dna ◽  
Specific Distribution

Mitochondrial DNA sequences can be transferred into the nuclear genome, giving rise to nuclear mitochondrial DNA sequences (NUMTs). NUMTs have been described in numerous eukaryotes. However, the studies on the distribution of NUMTs and its influencing factors are still inadequate and even controversial. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, in which we selected 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results showed that the contents of NUMTs varied greatly in these species, and bursts of NUMTs existed in some species or lineages. Further detailed analyses showed that the large number of NUMTs might be related to the large genomes; NUMTs tended to be inserted into unstable regions of the genomes; and the inserted NUMTs might also be affected by transposable elements (TEs) in the neighbors, leading to fragmentations and duplications, followed by bursts of NUMTs. In summary, our results suggest that a variety of genomic environmental factors can determine the insertion and post-insertion fate of NUMTs, resulting in their species- or lineage-specific distribution patterns, and that studying the evolution of NUMTs can provide good evidence and theoretical basis for exploring the dynamics of exogenous DNA entering into the nuclear genome.

Nine new species of the subgenus Stegana (Steganina) from China, with DNA barcoding information (Diptera: Drosophilidae)

Zootaxa ◽  
2019 ◽  
Vol 4576 (1) ◽  
pp. 81
Author(s):  
BINGXUE LI ◽  
YUAN ZHANG ◽  
HONGWEI CHEN
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Molecular Analysis ◽  
Dna Sequences ◽  
Mitochondrial Cytochrome ◽  
Neighbor Joining ◽  
Species Groups ◽  
Mtcoi Gene

Eleven (two known and nine new) species of the subgenus Stegana (Steganina) from China are described or redescribed: S. (S.) longifibula Takada, 1968, S. (S.) toyaensis Okada & Sidorenko, 1992, S. (S.) biflava sp. nov., S. (S.) flavivittata sp. nov., S. (S.) hirtifoliacea sp. nov., S. (S.) latitabula sp. nov., S. (S.) panda sp. nov., S. (S.) pinguifoliacea sp. nov., S. (S.) spatulata sp. nov., S. (S.) stachydifolia sp. nov. and S. (S.) unguiculata sp. nov.; they are assigned into the coleoptrata, ornatipes and undulata species groups, respectively. A total of 130 DNA sequences of partial mitochondrial cytochrome c oxidase subunit I (mtCOI) gene of 38 species (including the 11 species) of above-mentioned three groups are newly obtained in this study. These sequences and other available barcoding sequences of the three groups are involved in a molecular analysis using neighbor-joining (NJ) method, in order to assess the availability of DNA barcoding for delimiting the Steganina species. The result indicates that all the sampled Steganina morphospecies within the three groups are monophyletic.  

scholarly journals Hundreds of nuclear and plastid loci yield insights into orchid relationships

2020 ◽  
Author(s):  
Oscar Alejandro Pérez-Escobar ◽  
Steven Dodsworth ◽  
Diego Bogarín ◽  
Sidonie Bellot ◽  
Juan A. Balbuena ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Gene Trees ◽  
Deep Time ◽  
Plastid Genomes ◽  
Phylogenetic Informativeness ◽  
History Of ◽  
Phylogenetic Framework

ABSTRACTPremise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

scholarly journals Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS) and chloroplast (trnL-F) DNA sequences

2021 ◽  
Vol 13 (3) ◽  
pp. 11034
Author(s):  
Emre SEVINDIK ◽  
Melike AYDOGAN ◽  
Mehmet Y. PAKSOY
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nuclear Ribosomal Dna ◽  
Neighbor Joining ◽  
F Region ◽  
Brassicaceae Species ◽  
Nj Tree ◽  
Brassicaceae Family

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.

scholarly journals Gene Loss and Evolution of the Plastome

2019 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Awdhesh Kumar Mishra ◽  
Adil Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Dna Sequences ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
The Earth ◽  
Chloroplast Genomes ◽  
Duplication Events

AbstractChloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203–156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.

scholarly journals Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

2019 ◽  
Vol 48 (4) ◽  
pp. 1099-1106
Author(s):  
Emre Sevindik ◽  
Zehra Tuğba Murathan ◽  
Sümeyye Filiz ◽  
Kübra Yalçin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nucleotide Composition ◽  
Neighbor Joining ◽  
Sequencing Data ◽  
F Region ◽  
Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

scholarly journals El uso de secuencias génicas para estudios taxonómicos

2017 ◽  
pp. 137
Author(s):  
Dolores González
Keyword(s):  
Dna Sequences ◽  
Cladistic Analysis ◽  
Nuclear Genome ◽  
Restriction Enzymes ◽  
Dna Variation ◽  
Transfer Rnas ◽  
Taxonomic Research ◽  
Sampling Procedures ◽  
Rna Genes ◽  
Molecular Characters

During the last years, the use of molecular characters for taxonomic research has increased notably. Characters most commonly used come from restriction enzymes and sequencing of genes or particular DNA regions. Sequences present potential advantages over other molecular characters. This paper describes sampling procedures to detect DNA variation through sequencing. Among procedures for DNA sequencing, enzymatic methods are of generalized application, and the tendency is toward the use of non-radioactive markers and automated sequencing. A brief introduction to the different stages of cladistic analysis is also included, especially those required for DNA sequences. A revision of genes used in systematics is provided. The most common are the nuclear, mitochondrial and chloroplast ribosomal RNA genes, and the rbcL from chloroplast. Other genes under investigation are the globins and the alcohol dehydrogenase (from the nuclear genome), the cytochrome b and the transfer RNAs (from the mitochondrial genome), and the "matK" and the "rpo" (from the chloroplast genome).

scholarly journals DNA preserved in jetsam whale ambergris

2020 ◽  
Vol 16 (2) ◽  
pp. 20190819 ◽  
Author(s):  
Ruairidh Macleod ◽  
Mikkel-Holger S. Sinding ◽  
Morten Tange Olsen ◽  
Matthew J. Collins ◽  
Steven J. Rowland
Keyword(s):  
Natural Product ◽  
Dna Sequences ◽  
Reference Data ◽  
Nuclear Genome ◽  
Indirect Evidence ◽  
Sperm Whale ◽  
Physeter Macrocephalus ◽  
Sperm Whales ◽  
Ecological Mechanisms

Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zealand and Sri Lanka, and sequences from ambergris of a sperm whale beached in The Netherlands. The lipid-rich composition of ambergris facilitated high preservation-quality of endogenous DNA, upon which we performed shotgun Illumina sequencing. Alignment of mitochondrial and nuclear genome sequences with open-access reference data for multiple whale species confirms that all three jetsam samples derived originally from sperm whales ( Physeter macrocephalus ). Shotgun sequencing here also provides implications for metagenomic insights into ambergris-preserved DNA. These results demonstrate significant implications for elucidating the origins of jetsam ambergris as a prized natural product, and also for the understanding of sperm whale metabolism and diet, and the ecological mechanisms underlying these coproliths.

scholarly journals DNA replication and chromosome positioning throughout the interphase in three-dimensional space of plant nuclei

2020 ◽  
Vol 71 (20) ◽  
pp. 6262-6272 ◽  
Author(s):  
Alžběta Němečková ◽  
Veronika Koláčková ◽  
Jan Vrána ◽  
Jaroslav Doležel ◽  
Eva Hřibová
Keyword(s):  
Dna Replication ◽  
Genome Size ◽  
Dna Sequences ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Nuclear Genome ◽  
Replication Timing ◽  
Plant Genome ◽  
Interphase Chromosome ◽  
Three Dimensional Space

Abstract Despite much recent progress, our understanding of the principles of plant genome organization and its dynamics in three-dimensional space of interphase nuclei remains surprisingly limited. Notably, it is not clear how these processes could be affected by the size of a plant’s nuclear genome. In this study, DNA replication timing and interphase chromosome positioning were analyzed in seven Poaceae species that differ in their genome size. To provide a comprehensive picture, a suite of advanced, complementary methods was used: labeling of newly replicated DNA by ethynyl-2'-deoxyuridine, isolation of nuclei at particular cell cycle phases by flow cytometric sorting, three-dimensional immunofluorescence in situ hybridization, and confocal microscopy. Our results revealed conserved dynamics of DNA replication in all species, and a similar replication timing order for telomeres and centromeres, as well as for euchromatin and heterochromatin regions, irrespective of genome size. Moreover, stable chromosome positioning was observed while transitioning through different stages of interphase. These findings expand upon earlier studies in suggesting that a more complex interplay exists between genome size, organization of repetitive DNA sequences along chromosomes, and higher order chromatin structure and its maintenance in interphase, albeit controlled by currently unknown factors.

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