From The Cover: Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species

AbstractChimeric retroposition is a process by which RNA is reverse transcribed and the resulting cDNA is integrated into the genome along with flanking sequences. This process plays essential roles and drives genome evolution. Although the origination rates of chimeric retrogenes are high in plant genomes, the evolutionary patterns of the retrogenes and their parental genes are relatively uncharacterised in the rice genome. In this study, we evaluated the substitution ratio of 24 retrogenes and their parental genes to clarify their evolutionary patterns. The results indicated that seven gene pairs were under positive selection. Additionally, soon after new chimeric retrogenes were formed, they rapidly evolved. However, an unexpected pattern was also revealed. Specifically, after an undefined period following the formation of new chimeric retrogenes, the parental genes, rather than the new chimeric retrogenes, rapidly evolved under positive selection. We also observed that one retro chimeric gene (RCG3) was highly expressed in infected calli, whereas its parental gene was not. Finally, a comparison of our Ka/Ks analysis with that of other species indicated that the proportion of genes under positive selection is greater for chimeric retrogenes than for non-chimeric retrogenes in the rice genome.

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Evolutionary patterns of the Ediacara biota

AccessScience ◽

10.1036/1097-8542.yb100137 ◽

2015 ◽

Keyword(s):

Evolutionary Patterns ◽

Ediacara Biota

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Chromatin immunoprecipitation (ChIP) assay

Protocol Exchange ◽

10.1038/nprot.2009.11 ◽

2009 ◽

Cited By ~ 1

Author(s):

Zhongfu Ni ◽

Danny W.-K. Ng ◽

Jianxin Liu ◽

Z. Jeffrey Chen

Keyword(s):

Chromatin Immunoprecipitation ◽

Chip Assay

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Evolutionary Patterns of Retinal-Binding Pockets of Type I Rhodopsins and Their Functions†

Photochemistry and Photobiology ◽

10.1562/2006-02-14-ra-802 ◽

2006 ◽

Vol 82 (6) ◽

pp. 1426 ◽

Cited By ~ 1

Author(s):

Larisa Adamian ◽

Zheng Ouyang ◽

Yan Yuan Tseng ◽

Jie Liang

Keyword(s):

Type I ◽

Evolutionary Patterns ◽

Binding Pockets

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Comparative Analysis of Genetic and Morphological Variation within the Platanthera hyperborea Complex (Orchidaceae)

Systematic Botany ◽

10.1600/036364420x16033962925303 ◽

2020 ◽

Vol 45 (4) ◽

pp. 767-778

Author(s):

Eranga Wettewa ◽

Nick Bailey ◽

Lisa E. Wallace

Keyword(s):

North America ◽

Diploid Species ◽

Morphological Characters ◽

Evolutionary Patterns ◽

Founding Population ◽

Multiple Origins ◽

Geographic Structure ◽

Species Complexes ◽

Nuclear Its ◽

Cryptic Taxa

Abstract—Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, and P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America.

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