scholarly journals GeneSyn: a tool for detecting conserved gene order across genomes

2004 ◽  
Vol 20 (9) ◽  
pp. 1472-1474 ◽  
Author(s):  
G. Pavesi ◽  
G. Mauri ◽  
F. Iannelli ◽  
C. Gissi ◽  
G. Pesole
Keyword(s):  
Gene Order ◽  
Conserved Gene

scholarly journals Tight association of genome rearrangements with gene expression in conifer plastomes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chung-Shien Wu ◽  
Edi Sudianto ◽  
Shu-Miaw Chaw
Keyword(s):  
Gene Expression ◽  
Gene Order ◽  
Genomic Rearrangements ◽  
First Line ◽  
Conifer Species ◽  
Antisense Transcripts ◽  
Plastid Genomes ◽  
Rnaseq Data ◽  
Tight Association ◽  
Conserved Gene

Abstract Background Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. Results We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. Conclusions Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

Finding Conserved Gene Order Across Multiple Genomes

2007 ◽  
pp. 111-120
Author(s):  
Giulio Pavesi ◽  
Graziano Pesole
Keyword(s):  
Gene Order ◽  
Multiple Genomes ◽  
Conserved Gene

scholarly journals A Second-Generation Integrated Map of the Silkworm Reveals Synteny and Conserved Gene Order Between Lepidopteran Insects

Genetics ◽  
2006 ◽  
Vol 173 (3) ◽  
pp. 1319-1328 ◽  
Author(s):  
Yuji Yasukochi ◽  
Laksmikutty A. Ashakumary ◽  
Kotaro Baba ◽  
Atsuo Yoshido ◽  
Ken Sahara
Keyword(s):  
Gene Order ◽  
Second Generation ◽  
Integrated Map ◽  
Lepidopteran Insects ◽  
Conserved Gene

Another blow to the conserved gene order in Annelida: evidence from mitochondrial genomes of the calcareous tubeworm genus Hydroides

2021 ◽  
pp. 107124
Author(s):  
Yanan Sun ◽  
Guillemine Daffe ◽  
Yanjie Zhang ◽  
Joan Pons ◽  
Jian-Wen Qiu ◽  
...  
Keyword(s):  
Gene Order ◽  
Mitochondrial Genomes ◽  
Conserved Gene

scholarly journals Evaluation of the phylogenetic position of the sulfate-reducing bacterium Thermodesulfovibrio yellowstonii (phylum Nitrospirae) by means of gene order data from completely sequenced genomes

2010 ◽  
Vol 60 (5) ◽  
pp. 1090-1102 ◽  
Author(s):  
Takashi Kunisawa
Keyword(s):  
Gene Order ◽  
Common Ancestor ◽  
Evolutionary Relationship ◽  
Phylogenetic Position ◽  
Bacterial Genomes ◽  
Bacterial Phyla ◽  
Sulfate Reducing ◽  
Phylogenetic Placement ◽  
Conserved Gene ◽  
Group 1

The phylogenetic placement of Thermodesulfovibrio yellowstonii was investigated on the basis of gene order data from completely sequenced bacterial genomes. T. yellowstonii was found to share four gene arrangements characteristic of the Proteobacteria, Aquificae, Planctomycetes, Spirochaetes, Bacteroidetes, Chlorobi, Acidobacteria, Verrucomicrobia and termite group 1, the presence of which defines superphylum 2. The remaining phyla show sets of alternative gene arrangements and form superphylum 1. An analysis of conserved gene pairs showed that the overall genome organization of T. yellowstonii is most similar to that of deltaproteobacteria. Three arrangements that suggest gene translocations were identified that are likely to have occurred in a common ancestor of T. yellowstonii and the Proteobacteria exclusive of virtually all other major bacterial phyla. The translocation events suggest the closest evolutionary relationship between T. yellowstonii and the Proteobacteria.

Conservation of gene order in human microRNA-neighboring regions

Genome ◽  
2012 ◽  
Vol 55 (09) ◽  
pp. 701-704 ◽  
Author(s):  
Jianshu Chen ◽  
Wei Chen ◽  
Yudong Li
Keyword(s):  
Gene Order ◽  
Biological Function ◽  
Noncoding Rnas ◽  
Genomic Analysis ◽  
Unique Characteristic ◽  
Important Class ◽  
Human Mirnas ◽  
Genomic Architecture ◽  
Conserved Gene ◽  
Mouse Genomic

The biological function and evolution of microRNAs (miRNAs), an important class of noncoding regulatory genes, have attracted wide interest. However, their evolutionary impact on gene order rearrangements remains unknown. We examined the gene-order stability of miRNA-neighboring regions by a comparative human–mouse genomic analysis and found that the neighboring genes of human miRNAs tend to have a conserved gene order. This observation cannot be attributed to the functional bias of neighboring genes, and is a unique characteristic of miRNAs but not other noncoding RNAs. Our findings suggest that mammalian miRNAs stabilize the genomic architecture in evolution.

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