Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae)

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 634-641 ◽  
Author(s):  
T HM Mes ◽  
P Kuperus ◽  
J Kirschner ◽  
J Stepanek ◽  
P Oosterveld ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Hot Spot ◽  
Phylogenetic Signal ◽  
Direct Repeats ◽  
Nucleotide Substitutions ◽  
Replication Slippage ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Structural Mutations

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.Key words: Taraxacum, indel, non-coding chloroplast DNA, hairpin, evolution.

scholarly journals Deletion Formation Between the Two Salmonella typhimurium Flagellin Genes Encoded on the Mini F Plasmid: Escherichia coli ssb Alleles Enhance Deletion Rates and Change Hot-Spot Preference for Deletion Endpoints

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 563-572 ◽  
Author(s):  
Takafumi Mukaihara ◽  
Masatoshi Enomoto
Keyword(s):  
Escherichia Coli ◽  
Salmonella Typhimurium ◽  
Hot Spots ◽  
Hot Spot ◽  
Direct Repeats ◽  
Replication Slippage ◽  
Detection Systems ◽  
Deletion Formation ◽  
Homologous Sequences ◽  
Deletion Detection

Deletion formation between the 5′-mostly homologous sequences and between the 3′-homeologous sequences of the two Salmonella typhimurium flagellin genes was examined using plasmid-based deletion-detection systems in various Escherichia coli genetic backgrounds. Deletions in plasmid pLC103 occur between the 5′ sequences, but not between the 3′ sequences, in both RecA-independent and RecA-dependent ways. Because the former is predominant, deletion formation in a recA background depends on the length of homologous sequences between the two genes. Deletion rates were enhanced 30- to 50-fold by the mismatch repair defects, mutS, mutL and uvrD, and 250-fold by the ssb-3 allele, but the effect of the mismatch defects was canceled by the ΔrecA allele. Rates of the deletion between the 3′ sequences in plasmid pLC107 were enhanced 17- to 130-fold by ssb alleles, but not by other alleles. For deletions in pLC107, 96% of the endpoints in the recA+ background and 88% in ΔrecA were in the two hot spots of the 60- and 33-nucleotide (nt) homologous sequences, whereas in the ssb-3 background >50% of the endpoints were in four- to 14-nt direct repeats dispersed in the entire 3′ sequences. The deletion formation between the homeologous sequences is RecA-independent but depends on the length of consecutive homologies. The mutant ssb allele lowers this dependency and results in the increase in deletion rates. Roles of mutant SSB are discussed with relation to misalignment in replication slippage.

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.

Chloroplast genome differentiation in Asian cultivated rice

Genome ◽  
1991 ◽  
Vol 34 (5) ◽  
pp. 818-826 ◽  
Author(s):  
Takashige Ishii ◽  
Koichiro Tsunewaki
Keyword(s):  
Oryza Sativa ◽  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Restriction Endonuclease ◽  
Genetic Relationships ◽  
Restriction Endonuclease Analysis ◽  
Asian Countries ◽  
Genome Differentiation ◽  
Chloroplast Genomes ◽  
Endonuclease Analysis

Restriction endonuclease analysis of chloroplast DNA was carried out to clarify the chloroplast genome differentiation between Asian varieties of Oryza sativa. Based on the restriction fragment patterns obtained with six endonucleases, i.e., EcoRI, HindIII, PstI, PvuII, SmaI, and XhoI, chloroplast genomes of 68 local varieties from 15 Asian countries could be classified into five types (types 1, 3, 10, 11, and 12). Among these types, four length mutations and two base substitutions were found; these changes were located on the PstI physical map of rice chloroplast DNA. In a dendrogram showing genetic relationships among five chloroplast genomes, they are mainly divided into two groups, which we have named as the Japonica (types 1, 11, and 12) and Indica (types 3 and 10) chloroplast genome groups. Both groups are distributed widely in Asian countries. The Japonica isozyme group classified by J.C. Glaszmann (1985. Rice Genetics. International Rice Research Institute, Manila, Philippines, pp. 83–90) carries only the Japonica chloroplast genome, whereas the Indica isozyme group contains both Japonica and Indica chloroplast genomes.Key words: Oryza sativa, Asian varieties, chloroplast DNA, restriction endonuclease analysis, chloroplast genome differentiation.

scholarly journals Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 608
Author(s):  
Sang-Chul Kim ◽  
Jei-Wan Lee ◽  
Byoung-Ki Choi
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Ion Torrent Sequencing ◽  
Species Specific ◽  
Taxonomic Characterization

In the present study, chloroplast genome sequences of four species of Symplocos (S. chinensis for. pilosa, S. prunifolia, S. coreana, and S. tanakana) from South Korea were obtained by Ion Torrent sequencing and compared with the sequences of three previously reported Symplocos chloroplast genomes from different species. The length of the Symplocos chloroplast genome ranged from 156,961 to 157,365 bp. Overall, 132 genes including 87 functional genes, 37 tRNA genes, and eight rRNA genes were identified in all Symplocos chloroplast genomes. The gene order and contents were highly similar across the seven species. The coding regions were more conserved than the non-coding regions, and the large single-copy and small single-copy regions were less conserved than the inverted repeat regions. We identified five new hotspot regions (rbcL, ycf4, psaJ, rpl22, and ycf1) that can be used as barcodes or species-specific Symplocos molecular markers. These four novel chloroplast genomes provide basic information on the plastid genome of Symplocos and enable better taxonomic characterization of this genus.

scholarly journals Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes

2020 ◽  
Author(s):  
Jiao Peng ◽  
Yunlin Zhao ◽  
Meng Dong ◽  
Shiquan Liu ◽  
Zhiyuan Hu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Wild Species ◽  
Evolutionary Relationship ◽  
Acid Sites ◽  
Human Beings ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Linear Sequence ◽  
Chloroplast Genomes ◽  
Cultivated Species

Abstract Background: The cultivated tea is one of the most important economic and ecological trees distributing worldwide. The cultivated tea suffered from long-term targeted selection of traits and overexploitation of habitats by human beings, which may change the genetic structure. Chloroplast is an organelle with a conserved cyclic structure, and can help us better understand the evolutionary relationship of Camellia plants.Results: The study conducted comparative analysis and evolution analysis between cultivated tea and wild tea, and detected the evolution characteristic in cultivated tea. Chloroplast genome sizes of cultivated tea were slightly different, ranged from 157,025 bp to 157,085 bp. These cultivated species were more conservative than wild species, in terms of the genome length, genes number, genes arrangement and GC contents. However, the IRs length of cultivated species was about 20 bp shorter than that of C. sinensis var. sisnensis. We also found that the nucleotide diversity of 14 sequences in cultivated tea was higher than that of wild tea. These results provided the evidence on the variation of chloroplast genomes of cultivated tea. Detail analysis on the chloroplast genome variation and evolution of cultivated tea showed that 67 SNPs and 46 indels and 16 protein coding genes had nucleotide substitutions. The most comment variation gene was ycf1. It has the largest number of nucleotide substitutions. At the same time, in ycf1, five amino acid sites were exhibiting site-specific selection, and a 9 bp sequence insertion was found in the C. sinensis cultivar. Anhua. The phylogenetic tree constructed by ycf1 sequence shows that two cultivated tea were not completely clustered, and the evolutionary relationship between C. sinensis var. sisnensis and C. sinensis cultivar. Longjing is closer than that of C. sinensis cultivar. Anhua.Conclusions: The cultivated species were more conservative than wild species in terms of architecture and linear sequence order. The variation of chloroplast genome of cultivated tea was mainly manifested in the nucleotide polymorphism of some sequences. The ycf1 gene played an important role in the adaptive evolution of cultivated tea. These results provided evidence regarding the influence of human activities on tea.

scholarly journals The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3919 ◽  
Author(s):  
Hui Cheng ◽  
Jinfeng Li ◽  
Hong Zhang ◽  
Binhua Cai ◽  
Zhihong Gao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
Chloroplast Genomes

Compared with other members of the family Rosaceae, the chloroplast genomes ofFragariaspecies exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing ofFragariaspecies is needed. In this study, we sequenced the complete chloroplast genome ofF. × ananassa‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination ofde novoassembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of theF. × ananassa‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallestFragariachloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content inFragaria, particularly among three octoploid strawberries which wereF. × ananassa‘Benihoppe’,F.chiloensis(GP33) andF.virginiana(O477). However, when the sequences of the coding and non-coding regions ofF. × ananassa‘Benihoppe’ were compared in detail with those ofF.chiloensis(GP33) andF.virginiana(O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK,trnS-trnG,atpF-atpH,trnC-petN,trnT-psbDandtrnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genusFragaria.

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.

scholarly journals Comparative Chloroplast Genome Analysis of Rhubarb Botanical Origins and the Development of Specific Identification Markers

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2811 ◽  
Author(s):  
Yuxin Zhou ◽  
Jing Nie ◽  
Ling Xiao ◽  
Zhigang Hu ◽  
Bo Wang
Keyword(s):  
Chinese Medicine ◽  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Genetic Identification ◽  
Protein Coding ◽  
Variable Regions ◽  
Specific Identification ◽  
Coding Regions ◽  
Botanical Species ◽  
Chloroplast Genomes

Rhubarb is an important ingredient in traditional Chinese medicine known as Rhei radix et rhizome. However, this common name refers to three different botanical species with different pharmacological effects. To facilitate the genetic identification of these three species for their more precise application in Chinese medicine we here want to provide chloroplast sequences with specific identification sites that are easy to amplify. We therefore sequenced the complete chloroplast genomes of all three species and then screened those for suitable sequences describing the three species. The length of the three chloroplast genomes ranged from 161,053 bp to 161,541 bp, with a total of 131 encoded genes including 31 tRNA, eight rRNA and 92 protein-coding sequences. The simple repeat sequence analysis indicated the differences existed in these species, phylogenetic analyses showed the chloroplast genome can be used as an ultra-barcode to distinguish the three botanical species of rhubarb, the variation of the non-coding regions is higher than that of the protein coding regions, and the variations in single-copy region are higher than that in inverted repeat. Twenty-one specific primer pairs were designed and eight specific identification sites were experimentally confirmed that can be used as special DNA barcodes for the identification of the three species based on the highly variable regions. This study provides a molecular basis for precise medicinal plant selection, and supplies the groundwork for the next investigation of the closely related Rheum species comparing and correctly identification on these important medicinal species.

scholarly journals Assembly of the durian chloroplast genome using long PacBio reads

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jeremy R. Shearman ◽  
Chutima Sonthirod ◽  
Chaiwat Naktang ◽  
Duangjai Sangsrakru ◽  
Thippawan Yoocha ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Complete Sequence ◽  
Inverted Repeats ◽  
Direct Repeats ◽  
Durio Zibethinus ◽  
Chloroplast Genomes ◽  
Long Reads

Abstract We have assembled the complete sequence of the Durio zibethinus chloroplast genome using long PacBio reads. Durian is a valuable commercial tree that produces durian fruit, which is popular in Southeast Asia. The chloroplast genome assembled into a single 143 kb cyclic contig that contained 111 genes. There were 46 short direct repeats (45 to 586 bp) and five short inverted repeats (63 to 169 bp). The long reads that were used for the assembly span the entire chloroplast with > 10 kb overlaps and multiple long reads join the start of the contig to the end of the contig. The durian chloroplast was found to lack the large inverted repeat that is common in chloroplast genomes. An additional 24 durian varieties were sequenced and compared to the assembly and found to also lack the large inverted repeat. There were nine SNPs among the varieties.

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