Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 237-247 ◽  
Author(s):  
Ted HM Mes ◽  
Reinhard M Fritsch ◽  
Sven Pollner ◽  
Konrad Bachmann
Keyword(s):  
Concerted Evolution ◽  
Morphological Evolution ◽  
Restriction Analysis ◽  
Nuclear Genome ◽  
Restriction Enzymes ◽  
Border Region ◽  
Chloroplast Genomes ◽  
Central Asian ◽  
Its Regions ◽  
Chloroplast Haplotypes

Relationships based on PCR-RFLPs of non-coding regions of cpDNA indicate that some of the largest subgenera of the genus Allium and five of the largest sections of the Central Asian subg. Melanocrommyum are artificial. Internested synapomorphic mutations without homoplasy were found only in the chloroplast genomes of plants of subg. Melanocrommyum that occur in the border region of Tajikistan, Uzbekistan, Afghanistan, and Kyrgyzstan. Eighteen of 49 plants surveyed were polymorphic for their ITS regions. Even plants that had identical chloroplast genomes were polymorphic for nuclear ribosomal regions. These individuals had markedly different frequencies of ITS variants that were detected with various restriction enzymes. The geographic partitioning of chloroplast haplotypes and the fact that the ITS variants could not be ordered hierarchically can readily be envisioned to result from gene flow. Processes such as concerted evolution and parallel morphological evolution may also be partly responsible for the disconcordance of mutations in the chloroplast and nuclear genome. However, the chimeric nature of the nuclear ribosomal regions indicates that concerted evolution is not the dominating process in Allium subg. Melanocrommyum.Key words: polymorphic, phylogeny, restriction analysis.

scholarly journals Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shizhuo Xiao ◽  
Pan Xu ◽  
Yitong Deng ◽  
Xibin Dai ◽  
Lukuan Zhao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Structure ◽  
Chloroplast Genome ◽  
Wild Species ◽  
Ipomoea Batatas ◽  
Nuclear Genome ◽  
Ipomoea Trifida ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Chloroplast Dna Markers

Abstract Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.

MOLECULAR DEFECTS OF THE FACTOR IX GENE CAUSING SEVERE HAEMOPHILIA

1987 ◽  
Author(s):  
B M Ludwig ◽  
R Schwaab ◽  
H H Brackmann ◽  
H Egli ◽  
K Olek
Keyword(s):  
Restriction Analysis ◽  
Cdna Probe ◽  
Restriction Enzymes ◽  
Factor Ix ◽  
Functional Abnormality ◽  
Gene Deletions ◽  
Structural Alterations ◽  
Haemophilia B ◽  
Molecular Defects ◽  
Precise Data

Deficiency or functional abnormality of factor IX protein leads to the X-linked recessive haemorrhagic disorder known as haemophilia B. Using the factor IX cDNA probe pTG 397 we have studied DNA purified from 40 patients afflicted with haemophilia B. Restriction analysis was carried out using Eco RI, Taq I and Xmn I which give result to DNA fragments representing 99 % of the whole factor IX gene. Mapping the gene this way four patients were shown to have structural alterations in the factor IX gene. To obtain more precise data concerning these mutations we additionally used restriction enzymes Bgl II and Hind III.The results listed below indicate more patients have to be examined to conclude a strong correlation between inhibitors to factor IX and the presence of gross gene deletions. This view is supported by the findings that two further inhibitor forming patients had no sizable deletions.

scholarly journals DNA Analysis of Ralstonia solanacearum and Related Bacteria Based on 282-bp PCR-Amplified Fragment

Plant Disease ◽  
2003 ◽  
Vol 87 (11) ◽  
pp. 1337-1343 ◽  
Author(s):  
Joselito Villa ◽  
Kenichi Tsuchiya ◽  
Mitsuo Horita ◽  
Marina Natural ◽  
Nenita Opina ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Dna Analysis ◽  
Restriction Analysis ◽  
Polymerase Chain Reaction Amplification ◽  
Restriction Enzymes ◽  
The Philippines ◽  
Restriction Fragments ◽  
Group Iii ◽  
Group I ◽  
Group 2

Strains of Ralstonia solanacearum, Pseudomonas syzygii, and the blood disease bacterium (BDB) from different countries were tested for polymerase chain reaction amplification of the 282-bp fragment using the primer pair 759 and 760. These 282-bp fragments from 49 strains of R. solanacearum, six strains of P. syzygii, and two strains of BDB were sequenced. A phylogenetic tree was generated based on the sequence alignment. The R. solanacearum strains were divided into three groups. Group I was composed of strains belonging to biovars 3, 4, 5, and biovar N2 from Japan. Most of the strains from this group were of Asian origin except for two strains from Australia and Guyana (GMI 1000), the type strain. Group II was composed of strains belonging to biovars 1 and 2 and biovar N2 from Brazil. Group III was composed of strains belonging to biovar N2 from Japan and the Philippines. All strains of P. syzygii and BDB clustered in group III. Based on nucleotide differences of the 282-bp fragments, restriction enzyme NlaIII was capable of differentiating R. solanacearum strains into the three groups. Restriction analysis of 165 R. solanacearum isolates from the Philippines using NlaIII showed that all biovar 3 and 4 (group 1) strains had restriction fragments of 116 and 166 bp, strains belonging to biovars 1 and 2 (group 2) showed no restriction, and one strain belonging to biovar 2 (group 3) showed restriction fragments of 54 and 228 bp in size. Thus, NlaIII could be used for rapid differentiation of R. solanacearum strains. Additionally, other restriction enzymes, such as McrI, BsiEI, and MnlI could be used to differentiate R. solanacearum strains from P. syzygii strains.

scholarly journals The economics of organellar gene loss and endosymbiotic gene transfer

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Steven Kelly
Keyword(s):  
Gene Transfer ◽  
Nuclear Genome ◽  
Energy Budgets ◽  
Net Energy ◽  
Endosymbiotic Gene Transfer ◽  
Organellar Genomes ◽  
Chloroplast Genomes ◽  
Evolution Of Life ◽  
The Difference ◽  
Life On Earth

Abstract Background The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. Results Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell. Conclusion Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.

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 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 Gene Loss and Evolution of the Plastome

2020 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Adil Khan ◽  
Abdul Latif Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Inverted Repeats ◽  
Rbcl Gene ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
Chloroplast Genomes ◽  
Duplication Events

Abstract Chloroplasts are unique organelles within plant cells and are ultimately 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 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 CDS in the chloroplasts of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) that span across the lineages that comprise algae, bryophytes, pteridophytes, gymnosperm, angiosperms, magnoliids, and protists. Genome-wide analyses revealed that the loss of the Rbcl gene in parasitic and heterotrophic plant species occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; while 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 encoding 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 analysed 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. Additionally, our findings support the hypothesis that these recombination events are the most probable cause behind the dynamic loss of chloroplast genes and inverted repeats in different species.

scholarly journals Genetic Mapping in Onion: Insight to the Evolution of a Large Diploid Genome

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 596d-596
Author(s):  
Joseph J. King ◽  
Michael J. Havey
Keyword(s):  
Mapping Population ◽  
Nuclear Genome ◽  
Restriction Enzymes ◽  
Cdna Libraries ◽  
Rflp Markers ◽  
Structural Rearrangements ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Duplicated Loci ◽  
Bulb Color

The bulb onion (Allium cepa L.) is a diploid with an very large nuclear genome of 15300 Mbp/1C (107× arabidopsis, 16× tomato, 6× maize). We developed a low-density genetic map with morphological, RAPD, and RFLP markers to examine genome organization and to study QTL controlling phenotypically correlated bulb quality traits. A mapping population of 58 F3 families was derived from a cross of the inbreds Brigham Yellow Globe 15-23 (BYG) × Alisa Craig 43 (AC). These inbreds are distinct in solids, storability, pungency, and bulb shape. Analysis of 580 RAPD primers detected 53 (9%) polymorphisms between BYG and AC, but only 12 (2%) segregated at expected ratios among F3 families. Using probes from onion cDNA libraries and four restriction enzymes, 214 RFLPs were identified between mapping parents. A 112-point map includes 96 RFLPs, 13 RAPDs, a locus controlling complementary red bulb color, and two loci hybridizing with a clone of the enzyme alliinase (EC 4.4.1.4), which produces the flavors characteristic of Allium species. Duplicated loci were detected by ≈25% of RFLP probes and were unlinked, loosely linked (2 to 30 cM), or tightly linked (<2 cM). This frequency of duplication was comparable to species with polyploid ancestors (paleopolyploids) and was higher than that found in most true diploids. However, the distribution of duplicated loci suggests that, in contrast to whole genome duplications typical of paleopolyploids, the contemporary size and structure of the onion genome may be a product of intrachromosomal duplications (cryptopolyploidy) and subsequent structural rearrangements.

scholarly journals Identification of phytoplasma strains associated with witches’ broom and yellowing in Ziziphus jujube nurseries in Iran

2020 ◽  
Vol 59 (1) ◽  
pp. 55-61
Author(s):  
Ghobad BABAEI ◽  
Seyyed Alireza ESMAEILZADEH-HOSSEINI ◽  
Mahbobeh ZANDIAN ◽  
Vahid NIKBAKHT
Keyword(s):  
Restriction Analysis ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Reference Pattern ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
Rflp Profile ◽  
Ziziphus Jujube ◽  
East Of Iran ◽  
Virtual Rflp

Phytoplasma symptoms, including proliferation, witches’ broom, leaf rolling and yellowing, were observed in jujube (Ziziphus jujube) nurseries in the East of Iran. Total nucleic acid was extracted from symptomatic and symptomless plants, and was tested for phytoplasma presence using nested PCR. Amplicons of about 1.8 kb (primer pair P1/P7) and 1.25 kb (R16F2n/R16R2) were obtained from all symptomatic plants but not from symptomless plants. Restriction fragment length polymorphism (RFLP) analysis of R16F2n/R2 amplicons using KpnI, HaeIII, RsaI, AluI, HpaII, HhaI, TaqI, MseI, BfaI and ThaI restriction enzymes showed two RFLP patterns referable to 16SrI and 16SrVI phytoplasma groups. The consensus sequences of Z. jujube yellowing and witches’ broom of six samples correspond to ‘Candidatus Phytoplasma asteris’ and ‘Candidatus Phytoplasma trifolii’-related strains. Two R16F2n/R16R2 16S rDNA sequences representative of each RFLP profile, one each from witches’ broom (accession number MK379605) and yellowing (MK379604) host symptoms, were submitted to the GenBank. Phylogenetic analysis confirmed that the phytoplasma strains associated with jujube yellowing clustered within the 16SrI phytoplasma clade, and those associated with witches’ broom clustered within the 16SrVI clade. Restriction analysis confirmed that virtual RFLP patterns of the jujube yellowing and witches’ broom phytoplasma strains were identical to the reference pattern of 16SrI-B and 16SrVI-A. This is the first report of these phytoplasma strains associations with witches’ broom and yellowing in jujube plants.

scholarly journals Restriction analysis of genetic variability of Polish isolates of Tomato black ring virus.

2004 ◽  
Vol 51 (3) ◽  
pp. 673-681 ◽  
Author(s):  
Magdalena Jończyk ◽  
Natasza Borodynko ◽  
Henryk Pospieszny
Keyword(s):  
Restriction Analysis ◽  
Restriction Enzymes ◽  
Black Ring ◽  
Rt Pcr ◽  
Tomato Black Ring Virus ◽  
Genomic Rnas ◽  
Pcr Products ◽  
Biological Tests ◽  
Entire Sequence ◽  
Selection Of

Several different isolates of Tomato black ring virus (TBRV) have been collected in Poland from cucumber, tomato, potato and black locust plants. Biological tests showed some differences in the range of infected plants and the type of symptoms, which was the basis for selection of seven the most biologically different TBRV isolates. According to the sequence of TBRV-MJ, several primer pairs were designed and almost the entire sequence of both genomic RNAs was amplified. The RT-PCR products derived from all tested TBRV isolates were digested by restriction enzymes. On the basis of the restriction patterns, the variable and the conserved regions of the TBRV genome were defined and the relationships between the Polish TBRV isolates established.

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