Local repeat sequence organization of an intergenic spacer in the chloroplast genome ofChlamydomonas reinhardtii leads to DNA expansion and sequence scrambling: A complex mode of “copychoice replication”?

2001 ◽  
Vol 26 (5) ◽  
pp. 583-594 ◽  
Author(s):  
Mahendra D. Wagle ◽  
Subhojit Sen ◽  
Basuthkar J. Rao
Keyword(s):  
Chloroplast Genome ◽  
Intergenic Spacer ◽  
Repeat Sequence ◽  
Complex Mode ◽  
Sequence Organization ◽  
Sequence Scrambling

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 Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4186 ◽  
Author(s):  
Yanqiang Ding ◽  
Yang Fang ◽  
Ling Guo ◽  
Zhidan Li ◽  
Kaize He ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Morphological Characters ◽  
Repeat Sequence ◽  
Genome Comparison ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Effective Option ◽  
Total Dna

Background Phylogenetic relationship within different genera of Lemnoideae, a kind of small aquatic monocotyledonous plants, was not well resolved, using either morphological characters or traditional markers. Given that rich genetic information in chloroplast genome makes them particularly useful for phylogenetic studies, we used chloroplast genomes to clarify the phylogeny within Lemnoideae. Methods DNAs were sequenced with next-generation sequencing. The duckweeds chloroplast genomes were indirectly filtered from the total DNA data, or directly obtained from chloroplast DNA data. To test the reliability of assembling the chloroplast genome based on the filtration of the total DNA, two methods were used to assemble the chloroplast genome of Landoltia punctata strain ZH0202. A phylogenetic tree was built on the basis of the whole chloroplast genome sequences using MrBayes v.3.2.6 and PhyML 3.0. Results Eight complete duckweeds chloroplast genomes were assembled, with lengths ranging from 165,775 bp to 171,152 bp, and each contains 80 protein-coding sequences, four rRNAs, 30 tRNAs and two pseudogenes. The identity of L. punctata strain ZH0202 chloroplast genomes assembled through two methods was 100%, and their sequences and lengths were completely identical. The chloroplast genome comparison demonstrated that the differences in chloroplast genome sizes among the Lemnoideae primarily resulted from variation in non-coding regions, especially from repeat sequence variation. The phylogenetic analysis demonstrated that the different genera of Lemnoideae are derived from each other in the following order: Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia. Discussion This study demonstrates potential of whole chloroplast genome DNA as an effective option for phylogenetic studies of Lemnoideae. It also showed the possibility of using chloroplast DNA data to elucidate those phylogenies which were not yet solved well by traditional methods even in plants other than duckweeds.

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.

scholarly journals Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242591
Author(s):  
Jie Li ◽  
Guang-ying Ye ◽  
Hai-lin Liu ◽  
Zai-hua Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Protein Coding ◽  
Important Species ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Mutational Hotspots

Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.

ThepetFregion of the chloroplast genome from the diatomThalassiosira weissflogii: sequence, organization and phylogeny

1998 ◽  
Vol 33 (3) ◽  
pp. 203-211 ◽  
Author(s):  
Pulcherie Gueneau ◽  
François Morel ◽  
Julie Laroche ◽  
Deana Erdner
Keyword(s):  
Chloroplast Genome ◽  
Sequence Organization

scholarly journals Chloroplast Dna Sequences Confirmed Genetic Divergence Within Calypogeia Muelleriana (Calypogeiaceae, Marchantiophyta)

2013 ◽  
Vol 32 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Katarzyna Buczkowska ◽  
Patrycja Gonera ◽  
Alina Bączkiewicz ◽  
Stanisław Rosadziński ◽  
Mariola Rabska
Keyword(s):  
United Kingdom ◽  
North America ◽  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Genetic Divergence ◽  
Intergenic Spacer ◽  
Reference Species ◽  
Isozyme Markers ◽  
Chloroplast Dna Sequences

Abstract Nine species of the genus Calypogeia Raddi are currently known from Europe: C. azurea, C. integristipula, C. neesiana,C. suecica, C. muelleriana, C. sphagnicola, C. fissa, C. arguta, and C. azorica. Recently, another species, morphologically resembling C. muelleriana but genetically distinct from it, was detected using isozyme markers. In the present study, relationships between the newly detected species (C. sp. nov.) and typical C. muelleriana were analyzed using the DNA sequencesdata of three regions from the chloroplast genome: introns of trnG and trnL genes and intergenic spacer trnH-psbA. Calypogeia sp. nov. differs from C. muelleriana s. str. (typical form) in all examined chloroplast regions. It differs as well from C. azurea, which was used as a reference species. The number of fixed nucleotide differences between C. muelleriana s. str. and C. sp. nov. is almost the same as between C. muelleriana s. str. and C. azurea. The results of the present study suggest a closer affinity of C. sp. nov. to C. azurea than to C. muelleriana s. str. in Europe, C. muelleriana s. str. was noted in Poland, Germany, Holland, United Kingdom and Azores. Samples determined as C. sp. nov., besides Poland, were so far detected also in North America

Peach chloroplast genome variation architecture and phylogenomic signatures of cpDNA introgression in Prunus

2019 ◽  
Vol 99 (6) ◽  
pp. 885-896
Author(s):  
Mohamed Hamdy Amar ◽  
Mahmoud Magdy ◽  
Lu Wang ◽  
Hui Zhou ◽  
Beibei Zheng ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Prunus Persica ◽  
Gc Content ◽  
Size Variation ◽  
Intergenic Spacer ◽  
Phylogenomic Analysis ◽  
Single Nucleotide Variants ◽  
Prunus Species ◽  
Genome Size Variation ◽  
Essential Information

The complete chloroplast genome of peach provides essential information required for the assessment of phylogenetic relationships among Prunus species. Here, we compared the complete chloroplast DNA (cpDNA) genome between two peach cultivars and a wild relative, Prunus mira. The cpDNA genomes of the three peach specimens ranged from 157 330 to 157 744 bp in length and all contained 133 genes and 128 intergenic spacer (IGS) regions with an average GC content of 36.8%. The cpDNA genome of peach contained approximately 600 simple sequence repeats (SSRs), with hexa-nucleotide repeats being the most frequent microsatellites. Most SSRs have undergone divergence between cultivated and wild peaches. A total of 331 single nucleotide variants were identified in the cpDNA genomes. Fifty-one multiple-base pair indels were detected, which are mainly responsible for the cpDNA genome size variation. The cpDNA genomes contained 45 hypervariable regions, with 78% in the large single copy region (LSC). Phylogenomic analysis revealed that Prunus persica is more closely related to Prunus kansuensis than to other wild relatives, and a frequency of introgression of the chloroplast genome between Prunus species was deduced. Collectively, various genetic variations in the cpDNA genomes can serve as molecular markers for genomic studies of Prunus species, such as DNA barcoding, phylogeny, and systematics.

The petF region of the chloroplast genome from the diatom Thalassiosira weissflogii: sequence, organization and phylogeny

1998 ◽  
Vol 33 (3) ◽  
pp. 203-211 ◽  
Author(s):  
PULCHERIE GUENEAU ◽  
FRANÇOIS MOREL ◽  
JULIE LAROCHE ◽  
DEANA ERDNER
Keyword(s):  
Chloroplast Genome ◽  
Thalassiosira Weissflogii ◽  
Sequence Organization
Sign in / Sign up

Export Citation Format

Share Document