Intron evolution in a phylogenetic perspective: Divergent trends in the two copies of the duplicated def gene in Impatiens L. (Balsaminaceae)

2014 ◽  
Vol 52 (2) ◽  
pp. 134-148 ◽  
Author(s):  
Ute VOLKMAR ◽  
Erik F. SMETS ◽  
Henning LENZ ◽  
Steven B. JANSSENS
2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.


Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 1843-1851 ◽  
Author(s):  
John Parsch

AbstractIntron sizes show an asymmetrical distribution in a number of organisms, with a large number of “short” introns clustered around a minimal intron length and a much broader distribution of longer introns. In Drosophila melanogaster, the short intron class is centered around 61 bp. The narrow length distribution suggests that natural selection may play a role in maintaining intron size. A comparison of 15 orthologous introns among species of the D. melanogaster subgroup indicates that, in general, short introns are not under greater DNA sequence or length constraints than long introns. There is a bias toward deletions in all introns (deletion/insertion ratio is 1.66), and the vast majority of indels are of short length (<10 bp). Indels occurring on the internal branches of the phylogenetic tree are significantly longer than those occurring on the terminal branches. These results are consistent with a compensatory model of intron length evolution in which slightly deleterious short deletions are frequently fixed within species by genetic drift, and relatively rare larger insertions that restore intron length are fixed by positive selection. A comparison of paralogous introns shared among duplicated genes suggests that length constraints differ between introns within the same gene. The janusA, janusB, and ocnus genes share two short introns derived from a common ancestor. The first of these introns shows significantly fewer indels than the second intron, although the two introns show a comparable number of substitutions. This indicates that intron-specific selective constraints have been maintained following gene duplication, which preceded the divergence of the D. melanogaster species subgroup.


Author(s):  
Jennifer A. D. Colbourne ◽  
Alice M. I. Auersperg ◽  
Megan L. Lambert ◽  
Ludwig Huber ◽  
Christoph J. Völter

Phytotaxa ◽  
2016 ◽  
Vol 255 (2) ◽  
pp. 160 ◽  
Author(s):  
FANG WU ◽  
LI-WEI ZHOU ◽  
XIAO-HONG JI ◽  
XUE-MEI TIAN ◽  
SHUANG-HUI HE

Grammothele and Theleporus have a shallow pore surface, which makes them morphologically close to corticioid fungi. However, from a phylogenetic perspective, they are polyphyletic genera within the core polyporoid clade of the Polyporales. Eight specimens with a shallow pore surface from Hainan, southern China, were morphologically and phylogenetically studied. Among them, one was determined as Grammothele denticulata, four were identified as Theleporus membranaceus, and three are described as Grammothele hainanensis. G. hainanensis is characterized by the annual and resupinate basidiocarps with poroid to irpicoid hymenophore, a dimitic hyphal system with clamped generative hyphae and weakly dextrinoid skeletal hyphae, the presence of cystidioles, hyphal pegs and dendrohyphidia, and cylindrical, hyaline and thin-walled basidiospores. It is closely related to G. quercina in phylogeny. Morphologically, G. quercina differs in producing perennial basidiocarps with cream to pale greyish and larger pores. The morphological differences among the new species and other species were analyzed.


2009 ◽  
Vol 104 (3) ◽  
pp. 526-529 ◽  
Author(s):  
Josélio Maria Galvão de Araújo ◽  
Gonzalo Bello ◽  
Hermann Gonçalves Schatzmayr ◽  
Flávia Barreto dos Santos ◽  
Rita Maria Ribeiro Nogueira

2014 ◽  
Vol 25 (1) ◽  
pp. 100-110 ◽  
Author(s):  
Yu Sun ◽  
Carrie A. Whittle ◽  
Pádraic Corcoran ◽  
Hanna Johannesson

2007 ◽  
Vol 73 (3) ◽  
pp. 183-234 ◽  
Author(s):  
Javier Francisco-Ortega ◽  
Eugenio Santiago-Valentín ◽  
Pedro Acevedo-Rodríguez ◽  
Carl Lewis ◽  
John Pipoly ◽  
...  

2011 ◽  
Vol 50 ◽  
pp. 19-42 ◽  
Author(s):  
Elie Dassa

In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.


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