scholarly journals The eIF4F and eIFiso4F Complexes of Plants: An Evolutionary Perspective

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Ryan M. Patrick ◽  
Karen S. Browning
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Flowering Plants ◽  
Plant Genome ◽  
Target Point ◽  
Evolutionary Perspective ◽  
Initiation Factors ◽  
Eif4f Complex ◽  
History Of ◽  
Common Target

Translation initiation in eukaryotes requires a number of initiation factors to recruit the assembled ribosome to mRNA. The eIF4F complex plays a key role in initiation and is a common target point for regulation of protein synthesis. Most work on the translation machinery of plants to date has focused on flowering plants, which have both the eIF4F complex (eIF4E and eIF4G) as well as the plant-specific eIFiso4F complex (eIFiso4E and eIFiso4G). The increasing availability of plant genome sequence data has made it possible to trace the evolutionary history of these two complexes in plants, leading to several interesting discoveries. eIFiso4G is conserved throughout plants, while eIFiso4E only appears with the evolution of flowering plants. The eIF4G N-terminus, which has been difficult to annotate, appears to be well conserved throughout the plant lineage and contains two motifs of unknown function. Comparison of eIFiso4G and eIF4G sequence data suggests conserved features unique to eIFiso4G and eIF4G proteins. These findings have answered some questions about the evolutionary history of the two eIF4F complexes of plants, while raising new ones.

scholarly journals Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief ◽  
2018 ◽  
Vol 18 ◽  
pp. 1972-1975 ◽  
Author(s):  
Shaoyuan Wu ◽  
Scott Edwards ◽  
Liang Liu
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
History Of ◽  
Genome Scale

scholarly journals Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16751 ◽  
Author(s):  
Adam C. Silver ◽  
David Williams ◽  
Joshua Faucher ◽  
Amy J. Horneman ◽  
J. Peter Gogarten ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Aeromonas Veronii ◽  
Host Interaction ◽  
History Of ◽  
Complex Evolutionary History

scholarly journals Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

2016 ◽  
Author(s):  
Michael S. Barker ◽  
Zheng Li ◽  
Thomas I. Kidder ◽  
Chris R. Reardon ◽  
Zhao Lai ◽  
...  
Keyword(s):  
Gene Family ◽  
Linkage Map ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Nuclear Gene ◽  
Flowering Plants ◽  
The Family ◽  
History Of ◽  
Phylogenomic Analyses

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

scholarly journals A phylum-wide survey reveals multiple independent gains of head regeneration in Nemertea

2019 ◽  
Vol 286 (1898) ◽  
pp. 20182524 ◽  
Author(s):  
Eduardo E. Zattara ◽  
Fernando A. Fernández-Álvarez ◽  
Terra C. Hiebert ◽  
Alexandra E. Bely ◽  
Jon L. Norenburg
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Ability To Regenerate ◽  
History Of ◽  
Phylogenetic Framework ◽  
Regenerative Ability ◽  
Head Regeneration

Animals vary widely in their ability to regenerate, suggesting that regenerative ability has a rich evolutionary history. However, our understanding of this history remains limited because regenerative ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We assessed ability to regenerate heads and tails either through our own experiments or from literature reports for 35 species of Nemertea spanning the diversity of the phylum, including representatives of 10 families and all three orders. We generated a phylogenetic framework using sequence data to reconstruct the evolutionary history of head and tail regenerative ability across the phylum and found that all evaluated species can remake a posterior end but surprisingly few could regenerate a complete head. Our analysis reconstructs a nemertean ancestor unable to regenerate a head and indicates independent gains of head regenerative ability in at least four separate lineages, with one of these gains taking place as recently as the last 10–15 Myr. Our study highlights nemerteans as a valuable group for studying evolution of regeneration and identifying mechanisms associated with repeated gains of regenerative ability.

Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 411-416 ◽  
Author(s):  
Hikmet Budak ◽  
Robert C Shearman ◽  
Ismail Dweikat
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
Specific Marker ◽  
Buchloe Dactyloides ◽  
A Genome ◽  
Organelle Genomes ◽  
History Of

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalograss evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.Key words: buffalograss, evolution, organelle genomes, turfgrass.

scholarly journals Reconciliation of Sequence Data and Updated Annotation of the Genome of Agrobacterium tumefaciens C58, and Distribution of a Linear Chromosome in the Genus Agrobacterium

2012 ◽  
Vol 79 (4) ◽  
pp. 1414-1417 ◽  
Author(s):  
Steven Slater ◽  
João C. Setubal ◽  
Brad Goodner ◽  
Kathryn Houmiel ◽  
Jian Sun ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Evolutionary History ◽  
Sequence Data ◽  
Additional Analysis ◽  
Linear Chromosome ◽  
Content Type ◽  
History Of ◽  
Agrobacterium Tumefaciens C58

ABSTRACTTwo groups independently sequenced theAgrobacterium tumefaciensC58 genome in 2001. We report here consolidation of these sequences, updated annotation, and additional analysis of the evolutionary history of the linear chromosome, which is apparently limited to the biovar I group ofAgrobacterium.

scholarly journals Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

2007 ◽  
Vol 189 (21) ◽  
pp. 7932-7936 ◽  
Author(s):  
Tomoo Sawabe ◽  
Kumiko Kita-Tsukamoto ◽  
Fabiano L. Thompson
Keyword(s):  
Sequence Analysis ◽  
Evolutionary History ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Multilocus Sequence Analysis ◽  
Protein Coding ◽  
History Of

ABSTRACT We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br ).

scholarly journals Evolutionary History of Subtilases in Land Plants and Their Involvement in Symbiotic Interactions

2017 ◽  
Vol 30 (6) ◽  
pp. 489-501 ◽  
Author(s):  
Alexander Taylor ◽  
Yin-Long Qiu
Keyword(s):  
Evolutionary History ◽  
Arbuscular Mycorrhizae ◽  
Sequence Data ◽  
Land Plants ◽  
Mutualistic Symbiosis ◽  
Symbiotic Interactions ◽  
History Of ◽  
New Gene ◽  
Microbe Interactions ◽  
Origin Of Angiosperms

Subtilases, a family of proteases involved in a variety of developmental processes in land plants, are also involved in both mutualistic symbiosis and host-pathogen interactions in different angiosperm lineages. We examined the evolutionary history of subtilase genes across land plants through a phylogenetic analysis integrating amino acid sequence data from full genomes, transcriptomes, and characterized subtilases of 341 species of diverse green algae and land plants along with subtilases from 12 species of other eukaryotes, archaea, and bacteria. Our analysis reconstructs the subtilase gene phylogeny and identifies 11 new gene lineages, six of which have no previously characterized members. Two large, previously unnamed, subtilase gene lineages that diverged before the origin of angiosperms accounted for the majority of subtilases shown to be associated with symbiotic interactions. These lineages expanded through both whole-genome and tandem duplication, with differential neofunctionalization and subfunctionalization creating paralogs associated with different symbioses, including nodulation with nitrogen-fixing bacteria, arbuscular mycorrhizae, and pathogenesis in different plant clades. This study demonstrates for the first time that a key gene family involved in plant-microbe interactions proliferated in size and functional diversity before the explosive radiation of angiosperms.

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