Phylogenetic implication of the chloroplast rpoC1 intron loss in the Aizoaceae (Caryophyllales)

2007 ◽  
Vol 35 (6) ◽  
pp. 372-380 ◽  
Author(s):  
Joachim Thiede ◽  
Sabrina A. Schmidt ◽  
Barbara Rudolph
Keyword(s):  
Intron Loss ◽  
Phylogenetic Implication

The sugar beet mitochondrial nad4 gene: an intron loss and its phylogenetic implication in the Caryophyllales

2002 ◽  
Vol 104 (2) ◽  
pp. 209-213 ◽  
Author(s):  
N. Itchoda ◽  
S. Nishizawa ◽  
H. Nagano ◽  
T. Kubo ◽  
T. Mikami
Keyword(s):  
Sugar Beet ◽  
Intron Loss ◽  
Phylogenetic Implication ◽  
Nad4 Gene

scholarly journals Microhomology-Mediated Intron Loss during Metazoan Evolution

2013 ◽  
Vol 5 (6) ◽  
pp. 1212-1219 ◽  
Author(s):  
Robin van Schendel ◽  
Marcel Tijsterman
Keyword(s):  
Intron Loss ◽  
Metazoan Evolution

scholarly journals Complete mitochondrial genome of Procapra picticaudata, with phylogenetic implication

2019 ◽  
Vol 4 (2) ◽  
pp. 2347-2348
Author(s):  
Ke-Ji Guo ◽  
Hai-Jun Jiang ◽  
Feng-Jun Li ◽  
Zhi-Min Jiang ◽  
Shun-de Chen ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Phylogenetic Implication

scholarly journals The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xu Wang ◽  
Lihua Jia ◽  
Mingdao Wang ◽  
Hao Yang ◽  
Mingyue Chen ◽  
...  
Keyword(s):  
Large Scale ◽  
Core Protein ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Purifying Selection ◽  
Intron Loss ◽  
Gene Rearrangements ◽  
Total Size ◽  
Medicinal Fungus ◽  
Taiwanofungus Camphoratus

Abstract Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

scholarly journals Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina

2019 ◽  
Vol 20 (20) ◽  
pp. 5167 ◽  
Author(s):  
Qiang Li ◽  
Yuanhang Ren ◽  
Xiaodong Shi ◽  
Lianxin Peng ◽  
Jianglin Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Intron Loss ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Time ◽  
Dynamic Changes ◽  
Protein Coding ◽  
Tree Topologies ◽  
Nuclear Genomes

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

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