Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana

Anne-Marie van Dodeweerd; Caroline R Hall; Elisabeth G Bent; Samantha J Johnson; Michael W Bevan; Ian Bancroft

doi:10.1139/g99-033

Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana

Genome ◽

10.1139/g99-033 ◽

1999 ◽

Vol 42 (5) ◽

pp. 887-892 ◽

Cited By ~ 15

Author(s):

Anne-Marie van Dodeweerd ◽

Caroline R Hall ◽

Elisabeth G Bent ◽

Samantha J Johnson ◽

Michael W Bevan ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Dna Sequences ◽

Genomic Dna ◽

Genome Structure ◽

Plant Genome ◽

Fine Scale ◽

Plant Genomics ◽

Homologous Genes ◽

Conserved Genes ◽

Plant Genome Evolution

Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.

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Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativum L.)

Genome ◽

10.1139/g01-056 ◽

2001 ◽

Vol 44 (4) ◽

pp. 716-728 ◽

Cited By ~ 21

Author(s):

Pavel Neumann ◽

Marcela Nouzová ◽

Jirí Macas

Keyword(s):

Pisum Sativum ◽

Repetitive Dna ◽

Dna Sequences ◽

Genomic Dna ◽

Tandem Repeats ◽

Genomic Library ◽

Chromosome Morphology ◽

Plant Genome ◽

Genomic Repeats ◽

Dispersed Repeats

A set of pea DNA sequences representing the most abundant genomic repeats was obtained by combining several approaches. Dispersed repeats were isolated by screening a short-insert genomic library using genomic DNA as a probe. Thirty-two clones ranging from 149 to 2961 bp in size and from 1000 to 39 000/1C in their copy number were sequenced and further characterized. Fourteen clones were identified as retrotransposon-like sequences, based on their homologies to known elements. Fluorescence in situ hybridization using clones of reverse transcriptase and integrase coding sequences as probes revealed that corresponding retroelements were scattered along all pea chromosomes. Two novel families of tandem repeats, named PisTR-A and PisTR-B, were isolated by screening a genomic DNA library with Cot-1 DNA and by employing genomic self-priming PCR, respectively. PisTR-A repeats are 211212 bp long, their abundance is 2 × 104 copies/1C, and they are partially clustered in a secondary constriction of one chromosome pair with the rest of their copies dispersed on all chromosomes. PisTR-B sequences are of similar abundance (104 copies/1C) but differ from the "A" family in their monomer length (50 bp), high A/T content, and chromosomal localization in a limited number of discrete bands. These bands are located mainly in (sub)telomeric and pericentromeric regions, and their patterns, together with chromosome morphology, allow discrimination of all chromosome types within the pea karyotype. Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia.Key words: repetitive DNA, plant genome, retroelements, satellite DNA, Pisum sativum.

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PARALLEL SYNTENIC ALIGNMENTS

Parallel Processing Letters ◽

10.1142/s0129626403001604 ◽

2003 ◽

Vol 13 (04) ◽

pp. 689-703 ◽

Cited By ~ 3

Author(s):

NATSUHIKO FUTAMURA ◽

SRINIVAS ALURU ◽

XIAOQIU HUANG

Keyword(s):

Parallel Algorithm ◽

Dna Sequences ◽

Genomic Dna ◽

Sequential Algorithm ◽

Base Pairs ◽

Conserved Genes ◽

Alignment Problem ◽

Time Optimal ◽

High Degree ◽

Gene Rich Region

Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species and in identifying conserved genes. In this paper, we present a parallel algorithm for computing syntenic alignments that runs in [Formula: see text] time, where m and n are the respective lengths of the two genomic sequences, and p is the number of processors used. Our algorithm is time optimal with respect to the corresponding sequential algorithm and can use [Formula: see text] processors, where n is the length of the larger sequence. The space requirement of the algorithm is [Formula: see text] per processor. Using an implementation of this parallel algorithm, we report the alignment of a gene-rich region of human chromosome 12, namely 12p13 and its syntenic region in mouse chromosome 6 (both over 220,000 base pairs in length) in under 24 minutes on a 64-processor IBM xSeries cluster.

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Evidence for genetic diversity in Trypanosoma (Nannomonas) congolense

Parasitology ◽

10.1017/s0031182000051465 ◽

1986 ◽

Vol 93 (2) ◽

pp. 291-304 ◽

Cited By ~ 32

Author(s):

P. A. O. Majiva ◽

R. Hamers ◽

N. Van Meirvenne ◽

G. Matthyssens

Keyword(s):

Genetic Diversity ◽

Trypanosoma Brucei ◽

Restriction Enzyme ◽

Dna Sequences ◽

Genomic Dna ◽

Trypanosoma Congolense ◽

Synthetic Oligonucleotide ◽

Hybridization Probes ◽

Conserved Genes ◽

Variant Antigen

SUMMARYGenetic proximity between two karyotypic groups of Trypanosoma congolense was investigated using as hybridization probes: (i) total genomic DNA, (ii) a 35 nucleotide long synthetic oligonucleotide, and (iii) non-variant antigen type (non-VAT) specific complementary DNAs. The phylogenetic relationship between Trypanosoma brucei and T. evansi, both of which are accepted species in the subgenus Trypanozoon, was used as a reference to assess the phylogenetic proximity of the two groups of T. congolense. Results indicate that some morphologically indistinguishable T. congolense populations differ in a variety of molecular and genetic properties: molecular karyotypes, majority of the DNA sequences, and the restriction enzyme sites in the genomic environments of various conserved genes. The implications of these findings for trypanosome evolution and T. congolense epidemiology are discussed.

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Insights into the Structural and Functional Evolution of Plant Genomes Afforded by the Nucleotide Sequences of Chromosomes 2 and 4 of Arabidopsis thaliana

Yeast ◽

10.1155/2000/365024 ◽

2000 ◽

Vol 1 (1) ◽

pp. 1-5

Author(s):

Ian Bancroft

Keyword(s):

Arabidopsis Thaliana ◽

Sequence Data ◽

Plant Genome ◽

Gene Products ◽

Duplicated Genes ◽

Genetic Redundancy ◽

Macro Scale ◽

Genome Content ◽

High Level ◽

Plant Genome Evolution

The rapidly accumulating genome sequence data from the plant Arabidopsis thaliana allows more detailed analysis of genome content and organisation than ever bafore possible in plants. The genome shows a surprisingly high level of genetic redundancy, with as many as 75% of gene products showing signficant homology to another protien of A. thaliana. Many duplicated genes occur in arrays of conserved order and indicate that A. thaliana is likely to have had a tetraploid ancestor. Analysis of the divergence of duplicated genome segments leads to the prediction of two major modes of plant genome evolution: macro-scale duplication and rearrangement of chromosomes and micro-scale translocation, duplication and loss of individual genes or small groups of genes.

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The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

10.1101/2021.06.18.448592 ◽

2021 ◽

Author(s):

Jack S. Gisby ◽

Marco Catoni

Keyword(s):

Genome Evolution ◽

Dna Sequences ◽

Plant Genome ◽

Genome Plasticity ◽

High Similarity ◽

Chromosomal Dna ◽

Dna Transposons ◽

Automated Annotation ◽

Plant Genome Evolution

Pack-TYPE transposable elements (TEs) are a group of non-autonomous DNA transposons found in plants. These elements can efficiently capture and shuffle coding DNA across the host genome, accelerating the evolution of genes. Despite their relevance for plant genome plasticity, the detection and study of Pack-TYPE TEs are challenging due to the high similarity these elements have with genes. Here, we produced an automated annotation procedure designed to study Pack-TYPE elements and used it to successfully annotate and analyse more than 4000 new Pack-TYPE TEs in the rice and maize genomes. Our analysis indicates that Pack-TYPE TEs are an abundant and heterogeneous group of elements. We found that these elements are associated with all main superfamilies of Class II DNA transposons in plants and likely share a similar mechanism to capture new chromosomal DNA sequences. Furthermore, we report examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack-TYPE TEs in plant genome evolution.

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Genomic interspersions determine the size and complexity of transgene loci in transgenic plants produced by microprojectile bombardment

Genome ◽

10.1139/g01-040 ◽

2001 ◽

Vol 44 (4) ◽

pp. 691-697 ◽

Cited By ~ 32

Author(s):

Sergei K Svitashev ◽

David A Somers

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Tandem Repeats ◽

Microprojectile Bombardment ◽

Culture Conditions ◽

Plant Genome ◽

Dna Fragments ◽

Chromosomal Breakage ◽

Multiple Copies ◽

Transgene Locus

The structure of transgene loci in six transgenic allohexaploid oat (Avena sativa L.) lines produced using microprojectile bombardment was characterized using fluorescence in situ hybridization (FISH) on extended DNA fibers (fiber-FISH). The transgene loci in five lines were composed of multiple copies of delivered DNA interspersed with genomic DNA fragments ranging in size from ca. 3 kb to at least several hundred kilobases, and in greater numbers than detected using Southern blot analysis. Although Southern analysis predicted that the transgene locus in one line consisted of long tandem repeats of the delivered DNA, fiber-FISH revealed that the locus actually contained multiple genomic interspersions. These observations indicated that transgene locus size and structure were determined by the number of transgene copies and, possibly to a greater extent, the number and the length of interspersing genomic DNA sequences within the locus. Large genomic interspersions detected in several lines were most likely the products of chromosomal breakage induced either by tissue culture conditions or, more likely, by DNA delivery into the nucleus using microprojectile bombardment. We propose that copies of transgene along with other extrachromosomal DNA fragments are used as patches to repair double-strand breaks (DSBs) in the plant genome resulting in the formation of transgene loci.Key words: genetic transformation, microprojectile bombardment, transgenic oat, FISH, transgene locus structure.

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Localization of tandemly repeated DNA sequences in Arabidopsis thaliana

The Plant Journal ◽

10.1046/j.1365-313x.1991.00159.x ◽

1991 ◽

Vol 1 (2) ◽

pp. 159-166 ◽

Cited By ~ 14

Author(s):

J. Maluszynska ◽

J.S. Heslop-Harrison

Keyword(s):

Arabidopsis Thaliana ◽

Dna Sequences ◽

Repeated Dna ◽

Repeated Dna Sequences ◽

Tandemly Repeated Dna

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Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

Beni-Suef University Journal of Basic and Applied Sciences ◽

10.1186/s43088-020-00094-4 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Kuldeepsingh A. Kalariya ◽

Ram Prasnna Meena ◽

Lipi Poojara ◽

Deepa Shahi ◽

Sandip Patel

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Competitive Inhibition ◽

Sequence Data ◽

Homology Model ◽

Squalene Synthase ◽

Gymnema Sylvestre ◽

Gardenia Jasminoides ◽

Ramachandran Plots ◽

Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

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