| 25 matches found in 11 documents. Search time: 0.753 seconds. |
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Score: 10.00 |
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| Title: Nucleotide polymorphism in the Adh2 region of the wild rice Oryza rufipogon .
| | Author: Yoshida K Miyashita NT .
| | Journal: Theor . Appl . Genet . Citation: V : 111 ( 6 ) P : 1215-28 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16133310 Accession (PMID): 16133310 | | Abstract: DNA variation in the alcohol dehydrogenase ( Adh2 ) region of the wild rice Oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the DNA variation in these species .
A dimorphic pattern was detected in the Adh2 region of O rufipogon .
The silent nucleotide diversity ( pi ) in the Adh2 region in O rufipogon was 0 . 011 , which was higher than that of the Adh1 region in O rufipogon .
Especially , a high nucleotide diversity was detected at synonymous sites of the catalytic domain 1 .
Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region , indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types .
On the other hand , the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region .
The neutrality test of Fu and Li indicated significantly negative deviation from the neutral mutation model for the replacement sites of the Adh2 region .
This result suggests purifying selection on the replacement sites of the Adh2 region , as detected for the Adh1 region .
Significant linkage disequilibria ( 16 . 4% of the tests ) were detected between the Adh1 and Adh2 regions .
Even when nonrandom association was tested for the strains belonging to one of the divergent sequence types of the Adh2 region , significant interlocus linkage disequilibria were detected .
The close physical distance and/or epistasis between the two Adh regions could be invoked to explain these nonrandom associations . | Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region , indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types .
[ Sen. 1, subscore: 1.00 ]: DNA variation in the alcohol dehydrogenase ( Adh2 ) region of the wild rice Oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the DNA variation in these species .
[ Sen. 2, subscore: 1.00 ]: A dimorphic pattern was detected in the Adh2 region of O rufipogon .
[ Sen. 3, subscore: 1.00 ]: The silent nucleotide diversity ( pi ) in the Adh2 region in O rufipogon was 0 . 011 , which was higher than that of the Adh1 region in O rufipogon .
[ Sen. 6, subscore: 1.00 ]: On the other hand , the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region .
[ Sen. 7, subscore: 1.00 ]: The neutrality test of Fu and Li indicated significantly negative deviation from the neutral mutation model for the replacement sites of the Adh2 region .
[ Sen. 8, subscore: 1.00 ]: This result suggests purifying selection on the replacement sites of the Adh2 region , as detected for the Adh1 region .
[ Sen. 9, subscore: 1.00 ]: Significant linkage disequilibria ( 16 . 4% of the tests ) were detected between the Adh1 and Adh2 regions .
[ Sen. 10, subscore: 1.00 ]: Even when nonrandom association was tested for the strains belonging to one of the divergent sequence types of the Adh2 region , significant interlocus linkage disequilibria were detected .
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Score: 5.00 |
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| Title: Patterns of genetic diversification within the Adh gene family in the grasses ( Poaceae ) .
| | Author: Gaut BS Peek AS Morton BR Clegg MT .
| | Journal: Mol . Biol . Evol Citation: V : 16 ( 8 ) P : 1086-97 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10474904 Accession (PMID): 10474904 | | Abstract: We investigated the evolutionary dynamics of the Adh gene family within the grasses ( Poaceae ) , with the goal of using molecular evolutionary tools to understand the process of gene family diversification .
We analyzed 21 Adh sequences representing a broad array of grasses .
Phylogenetic analyses suggested that Adh duplicated into Adh1 and Adh2 before the radiation of the grasses roughly 65 MYA .
Gene structure , including intron length , has varied little over this period .
Conservation of intron length prompted investigation into the dynamics of intron evolution , particularly the ability of intron sequences to form secondary structures .
Intron sequences did not have an extremely high or low minimum free energy of folding relative to permuted sequences , suggesting that individual Adh introns do not evolve under secondary structural constraints .
For coding sequences , the diversification of Adh1 and Adh2 was marked by a shift in third-position G + C content .
This shift may reflect differential selection for codon use .
Diversification between Adh1 and Adh2 was also typified by a shift in nonsynonymous nucleotide substitution rates , but there was no evidence that relatively fast nonsynonymous nucleotide substitution rates in the Adh2 clade were a product of diversifying selection .
Gene conversion may have played a role in retarding diversification of Adh1 and Adh2 in rice , but there is no evidence of gene conversion between paralogs in other taxa .
Although the reasons for retention of two functional Adh genes remain obscure , we propose that a shift in gene expression was important for the retention of the two Adh gene copies within the grasses .
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[ Sen. 9, subscore: 2.00 ]: Diversification between Adh1 and Adh2 was also typified by a shift in nonsynonymous nucleotide substitution rates , but there was no evidence that relatively fast nonsynonymous nucleotide substitution rates in the Adh2 clade were a product of diversifying selection .
[ Sen. 3, subscore: 1.00 ]: Phylogenetic analyses suggested that Adh duplicated into Adh1 and Adh2 before the radiation of the grasses roughly 65 MYA .
[ Sen. 7, subscore: 1.00 ]: For coding sequences , the diversification of Adh1 and Adh2 was marked by a shift in third-position G + C content .
[ Sen. 10, subscore: 1.00 ]: Gene conversion may have played a role in retarding diversification of Adh1 and Adh2 in rice , but there is no evidence of gene conversion between paralogs in other taxa .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: Molecular analysis of an alcohol dehydrogenase-encoding genomic clone ( adh2 ) from rice .
| | Author: Xie Y Wu R | | Journal: Gene Citation: V : 87 ( 2 ) P : 185-91 Year: 1990 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub2332167 Accession (PMID): 2332167 | | Abstract: An alcohol dehydrogenase-encoding gene was isolated from a rice genomic library .
The coding region was sequenced , and the gene was identified as adh2 .
The nucleotide sequence of this gene contains an open reading frame which is interrupted by nine introns .
Sequences that are important for eukaryotic gene expression , eg the TATA box , polyadenylation signal , intron/exon junction and putative splicing branch sites , are found in the expected locations in the rice adh2 .
A sequence related to the hexanucleotide core of regulatory elements identified in anaerobically induced plant genes is also present in the 5 region of the rice adh2 . | Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The coding region was sequenced , and the gene was identified as adh2 .
[ Sen. 4, subscore: 1.00 ]: Sequences that are important for eukaryotic gene expression , eg the TATA box , polyadenylation signal , intron/exon junction and putative splicing branch sites , are found in the expected locations in the rice adh2 .
[ Sen. 5, subscore: 1.00 ]: A sequence related to the hexanucleotide core of regulatory elements identified in anaerobically induced plant genes is also present in the 5 region of the rice adh2 .
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Score: 2.00 |
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| Title: The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4 .
| | Author: Tarchini R Biddle P Wineland R Tingey S Rafalski A | | Journal: Plant Cell Citation: V : 12 ( 3 ) P : 381-91 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10715324 Accession (PMID): 10715324 | | Abstract: A 2 . 3-centimorgan ( cM ) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced , revealing the presence of 33 putative genes , including several apparently involved in disease resistance .
Fourteen of the genes were confirmed by identifying the corresponding transcripts .
Five genes , spanning 1 . 9 cM of the region , cross-hybridized with maize genomic DNA and were genetically mapped in maize , revealing a stretch of colinearity with maize chromosome 4 .
The Adh1 gene marked one significant interruption .
This gene mapped to maize chromosome 1 , indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum .
Several other genes , most notably genes similar to known disease resistance genes , showed no cross-hybridization with maize genomic DNA , suggesting sequence divergence or absence of these sequences in maize , which is in contrast to several other well-conserved genes , including Adh1 and Adh2 .
These findings indicate that the use of rice as the model system for other cereals may sometimes be complicated by the presence of rapidly evolving gene families and microtranslocations .
Seven retrotransposons and eight transposons were identified in this rice segment , including a Tc1/Mariner-like element , which is new to rice .
In contrast to maize , retroelements are less frequent in rice .
Only 14 . 4% of this genome segment consist of retroelements .
Miniature inverted repeat transposable elements were found to be the most frequently occurring class of repetitive elements , accounting for 18 . 8% of the total repetitive DNA . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A 2 . 3-centimorgan ( cM ) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced , revealing the presence of 33 putative genes , including several apparently involved in disease resistance .
[ Sen. 6, subscore: 1.00 ]: Several other genes , most notably genes similar to known disease resistance genes , showed no cross-hybridization with maize genomic DNA , suggesting sequence divergence or absence of these sequences in maize , which is in contrast to several other well-conserved genes , including Adh1 and Adh2 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Gene targeting by homologous recombination as a biotechnological tool for rice functional genomics .
| | Author: Terada R Johzuka-Hisatomi Y Saitoh M Asao H Iida S | | Journal: Plant Physiol Citation: V : 144 P : 846-56 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17449652 Accession (PMID): 17449652 | | Abstract: The modification of an endogenous gene into a designed sequence by homologous recombination , termed gene targeting ( GT ) , has broad implications for basic and applied research .
Rice ( Oryza sativa ) , with a sequenced genome of 389 Mb , is one of the most important crops and a model plant for cereals , and the single-copy gene Waxy on chromosome 6 has been modified with a frequency of 1% per surviving callus by GT using a strong positive-negative selection .
Because the strategy is independent of gene-specific selection or screening , it is in principle applicable to any gene .
However , a gene in the multigene family or a gene carrying repetitive sequences may preclude efficient homologous recombination-promoted GT due to the occurrence of ectopic recombination .
Here , we describe an improved GT procedure whereby we obtained nine independent transformed calli having the alcohol dehydrogenase2 ( Adh2 ) gene modified with a frequency of approximately 2% per surviving callus and subsequently isolated eight fertile transgenic plants without the concomitant occurrence of undesirable ectopic events , even though the rice genome carries four Adh genes , including a newly characterized Adh3 gene , and a copy of highly repetitive retroelements is present adjacent to the Adh2 gene .
The results indicate that GT using a strong positive-negative selection can be widely applicable to functional genomics in rice and presumably in other higher plants .
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[ Sen. 5, subscore: 2.00 ]: Here , we describe an improved GT procedure whereby we obtained nine independent transformed calli having the alcohol dehydrogenase2 ( Adh2 ) gene modified with a frequency of approximately 2% per surviving callus and subsequently isolated eight fertile transgenic plants without the concomitant occurrence of undesirable ectopic events , even though the rice genome carries four Adh genes , including a newly characterized Adh3 gene , and a copy of highly repetitive retroelements is present adjacent to the Adh2 gene .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
