Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

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Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana

Theoretical and Applied Genetics ◽

10.1007/s00122-002-1183-y ◽

2003 ◽

Vol 106 (7) ◽

pp. 1256-1265 ◽

Cited By ~ 44

Author(s):

H. H. Yan ◽

J. Mudge ◽

D.-J. Kim ◽

D. Larsen ◽

R. C. Shoemaker ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Glycine Max ◽

Medicago Truncatula

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Comparative Genomics of Glycine max, Medicago truncatula, Other Legumes, and Arabidopsis thaliana

Legume Crop Genomics ◽

10.1201/9781439822265.ch9 ◽

2004 ◽

Author(s):

Nevin Dale Young

Keyword(s):

Arabidopsis Thaliana ◽

Glycine Max ◽

Comparative Genomics ◽

Medicago Truncatula

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Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/161.3.1269 ◽

2002 ◽

Vol 161 (3) ◽

pp. 1269-1278 ◽

Cited By ~ 7

Author(s):

Bernhard Haubold ◽

Jürgen Kroymann ◽

Andreas Ratzka ◽

Thomas Mitchell-Olds ◽

Thomas Wiehe

Keyword(s):

Genetic Diversity ◽

Arabidopsis Thaliana ◽

Linkage Disequilibrium ◽

Gene Conversion ◽

Genomic Sequence ◽

Genomic Region ◽

Resistance To Herbivory ◽

Linkage Disequilibria ◽

Coalescent Simulations ◽

The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

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Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays

Genome Biology ◽

10.1186/gb-2008-9-3-r57 ◽

2008 ◽

Vol 9 (3) ◽

pp. R57 ◽

Cited By ~ 11

Author(s):

Lei Li ◽

Hang He ◽

Juan Zhang ◽

Xiangfeng Wang ◽

Sulan Bai ◽

...

Keyword(s):

Glycine Max ◽

Medicago Truncatula ◽

Transcriptional Analysis ◽

Tiling Microarrays ◽

Syntenic Regions

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Genomic Background Predicts the Fate of Duplicated Genes: Evidence From the Yeast Genome

Genetics ◽

10.1093/genetics/166.4.1995 ◽

2004 ◽

Vol 166 (4) ◽

pp. 1995-1999 ◽

Cited By ~ 1

Author(s):

Ze Zhang ◽

Hirohisa Kishino

Keyword(s):

Recombination Rate ◽

Evolutionary Rate ◽

Average Rate ◽

Classical Model ◽

Purifying Selection ◽

Genomic Region ◽

Yeast Genome ◽

Duplicated Genes ◽

Potential Force ◽

Accelerated Evolution

Abstract Gene duplication with subsequent divergence plays a central role in the acquisition of genes with novel function and complexity during the course of evolution. With reduced functional constraints or through positive selection, these duplicated genes may experience accelerated evolution. Under the model of subfunctionalization, loss of subfunctions leads to complementary acceleration at sites with two copies, and the difference in average rate between the sequences may not be obvious. On the other hand, the classical model of neofunctionalization predicts that the evolutionary rate in one of the two duplicates is accelerated. However, the classical model does not tell which of the duplicates experiences the acceleration in evolutionary rate. Here, we present evidence from the Saccharomyces cerevisiae genome that a duplicate located in a genomic region with a low-recombination rate is likely to evolve faster than a duplicate in an area of high recombination. This observation is consistent with population genetics theory that predicts that purifying selection is less effective in genomic regions of low recombination (Hill-Robertson effect). Together with previous studies, our results suggest the genomic background (e.g., local recombination rate) as a potential force to drive the divergence between nontandemly duplicated genes. This implies the importance of structure and complexity of genomes in the diversification of organisms via gene duplications.

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Cloning and Functional Identification of Phosphoethanolamine Methyltransferase in Soybean (Glycine max)

Frontiers in Plant Science ◽

10.3389/fpls.2021.612158 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaomin Ji ◽

Xiaoyue Wu ◽

Wei Chen ◽

Qianhui Yuan ◽

Yixin Shen ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Glycine Max ◽

Stress Response ◽

Cell Metabolism ◽

Plant Stress ◽

Lipid Synthesis ◽

Normal Growth ◽

Functional Identification ◽

Short Root ◽

Response Elements

Phosphoethanolamine methyltransferase (PEAMT), a kind of S-adenosylmethionine-dependent methyltransferases, plays an essential role in many biological processes of plants, such as cell metabolism, stress response, and signal transduction. It is the key rate-limiting enzyme that catalyzes the three-step methylation of ethanolamine-phosphate (P-EA) to phosphocholine (P-Cho). To understand the unique function of PEAMT in soybean (Glycine max) lipid synthesis, we cloned two phosphoethanolamine methyltransferase genes GmPEAMT1 and GmPEAMT2, and performed functional identification. Both GmPEAMT1 and GmPEAMT2 contain two methyltransferase domains. GmPEAMT1 has the closest relationship with MtPEAMT2, and GmPEAMT2 has the closest relationship with CcPEAMT. GmPEAMT1 and GmPEAMT2 are located in the nucleus and endoplasmic reticulum. There are many light response elements and plant hormone response elements in the promoters of GmPEAMT1 and GmPEAMT2, indicating that they may be involved in plant stress response. The yeast cho2 opi3 mutant, co-expressing Arabidopsis thaliana phospholipid methyltransferase (PLMT) and GmPEAMT1 or GmPEAMT2, can restore normal growth, indicating that GmPEAMTs can catalyze the methylation of phosphoethanolamine to phosphate monomethylethanolamine. The heterologous expression of GmPEAMT1 and GmPEAMT2 can partially restore the short root phenotype of the Arabidopsis thaliana peamt1 mutant, suggesting GmPEAMTs have similar but different functions to AtPEAMT1.

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CHARACTERISTICS OF MIRNA BINDING SITES IN MRNAS OF MYB GENES OF ARABIDOPSIS, SOYA AND GRAPE

BIOTECHNOLOGY: STATE OF THE ART AND PERSPECTIVES ◽

10.37747/2312-640x-2021-19-205-206 ◽

2021 ◽

Vol 1 (19) ◽

pp. 205-206

Author(s):

I.V. Pinskiy

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factor ◽

Glycine Max ◽

Vitis Vinifera ◽

Binding Sites ◽

Myb Transcription Factor ◽

Transcription Factor Genes ◽

Myb Genes

The characteristics of various miRNA binding sites in the mRNAs of the MYB transcription factor genes of Arabidopsis thaliana, Glycine max and Vitis vinifera have been established. The most conserved miRNA binding sites were the binding sites of the miR828 family.

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