scholarly journals Sequence diversity of two chloroplast genes: rps4 and tRNAGly (UCC), in the liverwort Marchantia polymorpha, an emerging plant model system

2018 ◽  
Vol 87 (1) ◽  
Author(s):  
Hanna Kijak ◽  
Weronika Łodyga ◽  
Ireneusz J. Odrzykoski
Keyword(s):  
Chloroplast Genome ◽  
Sequence Variation ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Marchantia Polymorpha ◽  
Homologous Sequences ◽  
Clonal Lines ◽  
Suspension Line ◽  
Marchantia Paleacea ◽  
Almost All

<p>The primary purpose of this study is to evaluate the sequence variation for two regions of chloroplast DNA in a collection of 27 taxonomically well-annotated clonal lines of <em>Marchantia polymorpha</em> sensu lato derived from European populations. We attempted to develop molecular markers so as to identify three taxa usually recognized as subspecies. We sequenced two regions: the <em>rps4</em> gene along with the <em>rps4-trnT</em> intergenic spacer and an intron of the tRNA<sup>Gly</sup> (UCC) gene. Samples of <em>Marchantia paleacea</em> ssp. <em>diptera</em> from Japan were used for comparative purposes.</p><p>Three haplotypes (MA, MB, and MC) were identified for the species, and almost all sequence divergence between subspecies was found to occur at the level of 0.0023–0.0032 substitutions per site. The sequence divergence between <em>M. polymorpha</em> and <em>M. paleacea</em> was tenfold greater (0.0331–0.0340). We did not detect any differences between <em>M. paleacea</em> and homologous sequences from the reference chloroplast genome of <em>M. polymorpha</em> obtained from the GeneBank (NC_001319). It was confirmed that the cell suspension line A-18 used for the sequencing of the full chloroplast genome in 1986 was incorrectly taxonomically annotated.</p>

scholarly journals Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yun Song ◽  
Yongjiang Zhang ◽  
Jin Xu ◽  
Weimin Li ◽  
MingFu Li
Keyword(s):  
Chloroplast Genome ◽  
Size Structure ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Dna Barcodes ◽  
Ecological Value ◽  
Accurate Identification ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications

AbstractThe pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

A variable minisatellite sequence in the chloroplast genome of Sorbus L. (Rosaceae: Maloideae)

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 570-576 ◽  
Author(s):  
R Andrew King ◽  
Colin Ferris
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Chloroplast Genome ◽  
Length Polymorphism ◽  
Sequence Variation ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Chloroplast Microsatellites ◽  
Sorbus Aucuparia ◽  
Pcr Product ◽  
Restriction Fragment Length

The chloroplast genome is now known to be more variable than was once thought. Reports of RFLP (restriction fragment length polymorphism) and sequence variation, as well as variation in chloroplast microsatellites, are common. Here, data are presented on the variability of a minisatellite sequence in the chloroplast genome of Sorbus species. RFLP analysis of a PCR product comprising the region between the trnM and rbcL genes of nine Sorbus species identified seven size variants. Sequencing revealed the observed size polymorphism to be due to differences in the number of copies of an imperfect 9-bp motif. A more intensive survey of the variability of the minisatellite was undertaken in populations of Sorbus aucuparia. The potential uses of such regions in chloroplast DNA are discussed and a possible mechanism for the evolution of the minisatellite is presented.Key words: atpE, homoplasy, microsatellite, rowan, VNTR.

Sequence variation and evolution of nuclear DNA in man and the primates

1981 ◽  
Vol 292 (1057) ◽  
pp. 133-142 ◽  
Keyword(s):  
Dna Sequence ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Sequence Divergence ◽  
Gene Arrangement ◽  
Human Populations ◽  
Genetic Changes ◽  
Detailed Structural Analysis ◽  
Dna Sequence Variation ◽  
History Of

Recent advances in nucleic acid technology have facilitated the detection and detailed structural analysis of a wide variety of genes in higher organisms, including those in man. This in turn has opened the way to an examination of the evolution of structural genes and their surrounding and intervening sequences. In a study of the evolution of haemoglobin genes and neighbouring sequences in man and the primates, we have investigated gene arrangement and DNA sequence divergence both within and between species ranging from Old World monkeys to man. This analysis is beginning to reveal the evolutionary constraints that have acted on this region of the genome during primate evolution. Furthermore, DNA sequence variation, both within and between species, provides, in principle, a novel and powerful method for determining inter-specific phylogenetic distances and also for analysing the structure of present-day human populations. Application of this new branch of molecular biology to other areas of the human genome should prove important in unravelling the history of genetic changes that have occurred during the evolution of man.

scholarly journals Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2165 ◽  
Author(s):  
Xiao Zhang ◽  
Tao Zhou ◽  
Jia Yang ◽  
Jingjing Sun ◽  
Miaomiao Ju ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Sequence Divergence ◽  
Economic Plant ◽  
Genome Sequences ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Representative Species ◽  
Translation Initiation Codon

Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.

New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Parasitology ◽  
2012 ◽  
Vol 139 (8) ◽  
pp. 1063-1073 ◽  
Author(s):  
K. CWIKLINSKI ◽  
F. N. J. KOOYMAN ◽  
D. C. K. VAN DOORN ◽  
J. B. MATTHEWS ◽  
J. E. HODGKINSON
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Sequence Variation ◽  
Intergenic Spacer ◽  
Parasitic Nematodes ◽  
Sequence Information ◽  
Detailed Knowledge ◽  
Life Cycle Stages ◽  
Third Stage ◽  
Specific Variation

SUMMARYCyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3–62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means†.

Intra- and inter-specific mitochondrial DNA sequence divergence in Salmo: rainbow, steelhead, and cutthroat trouts

1985 ◽  
Vol 63 (9) ◽  
pp. 2088-2094 ◽  
Author(s):  
Gary M. Wilson ◽  
W. Kelley Thomas ◽  
Andrew T. Beckenbach
Keyword(s):  
Mitochondrial Dna ◽  
Rainbow Trout ◽  
Life Histories ◽  
Sequence Divergence ◽  
Cutthroat Trout ◽  
Restriction Enzymes ◽  
Restriction Endonuclease Analysis ◽  
Salmo Gairdneri ◽  
Intraspecific Divergence ◽  
Clonal Lines

Two forms of Salmo gairdneh with different life histories (steelhead and rainbow trout) were compared using restriction endonuclease analysis of mitochondrial DNA. A total of 19 individuals from four populations were studied for each of the two forms, using 14 restriction enzymes. In addition, five cutthroat trout samples were included as an interspecific comparison. These enzymes revealed a total of 81 cut sites, representing a sample of more than 400 nucleotides per fish. Of these sites, 25 were phylogenetically informative, dividing the 43 fish into 10 clonal lines, 8 Salmo gairdneri and 2 Salmo clarki. Results indicated detectable divergence between all geographic populations of steelhead and rainbow trout except Pennask rainbow trout, Coquihalla steelhead, and Wampus Creek rainbow trout. Other steelhead populations analysed showed a closer phylogenetic relationship to each other than to rainbow trout populations analysed. Intraspecific divergence was in most cases 1% or less, with a 1.5% maximum. Interspecific divergence between S. gairdneri and S. clarki was between 2% and 3.5%.

scholarly journals Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines

2010 ◽  
Vol 19 ◽  
pp. 100-114 ◽  
Author(s):  
J. B. WHITTALL ◽  
J. SYRING ◽  
M. PARKS ◽  
J. BUENROSTRO ◽  
C. DICK ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Sequence Divergence ◽  
Pine Needle ◽  
Chloroplast Genome Sequence

Characterization of a major tandemly repeated DNA sequence (RBMII) prevalent among many species of waterfowl (Anatidae)

Genome ◽  
1992 ◽  
Vol 35 (6) ◽  
pp. 1037-1044 ◽  
Author(s):  
Cort S. Madsen ◽  
Kevin P. McHugh ◽  
Siwo R. de Kloet
Keyword(s):  
Dna Sequence ◽  
Sequence Variation ◽  
Sequence Divergence ◽  
Repeated Dna ◽  
Sequence Comparisons ◽  
Nonrandom Distribution ◽  
Repeated Dna Sequence ◽  
Tandemly Repeated Dna Sequence ◽  
Tandemly Repeated Dna

We have investigated the evolution of a 190 base pair tandemly repeated DNA sequence (RBMII) in 27 different species of waterfowl. In this paper we show that the RBMII sequence is present in many species belonging to 7 of the 11 Anatid tribes. Inter- and intra-tribal differences in repeat presence indicate that, although the RBMII sequence has been maintained among widely divergent species, it is rapidly evolving. Restriction enzyme analyses suggest very different hierarchical repeat organizations among different species. DNA sequence comparisons of 32 cloned monomer units from five different species revealed what appears to be a nonrandom distribution of sequence divergence, as well as large differences (up to 25-fold) in intraspecific sequence variation between relatively closely related species.Key words: repeated DNA, Anatidae, sequence variation.

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