Phylogenetic classification of Pleurothecium and Pleurotheciella gen. nov. and its dactylaria-like anamorph (Sordariomycetes) based on nuclear ribosomal and protein-coding genes

Mycologia ◽  
2012 ◽  
Vol 104 (6) ◽  
pp. 1299-1314 ◽  
Author(s):  
Martina Réblová ◽  
Keith A. Seifert ◽  
Jacques Fournier ◽  
Václav Štěpánek
Keyword(s):  
Protein Coding ◽  
Phylogenetic Classification ◽  
Protein Coding Genes

scholarly journals Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Joonhyung Jung ◽  
Changkyun Kim ◽  
Joo-Hwan Kim
Keyword(s):  
Nucleotide Diversity ◽  
Structural Variations ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Protein ◽  
Genome Data ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Current Classification

Abstract Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

Description and phylogenetic classification of Stackelberginia cerberus sp. nov. (Diptera: Asilidae), comprising the first record of this genus from the Nearctic

Zootaxa ◽  
2017 ◽  
Vol 4306 (4) ◽  
pp. 567 ◽  
Author(s):  
TRISTAN A. MCKNIGHT ◽  
ROBERT A. CANNINGS
Keyword(s):  
Central Asia ◽  
Nuclear Protein ◽  
First Record ◽  
Morphological Characters ◽  
Western Hemisphere ◽  
Protein Coding ◽  
Mitochondrial Coi ◽  
Late Autumn ◽  
Phylogenetic Classification

Stackelberginia cerberus sp. nov. (Diptera: Asilidae) is described from the Amargosa desert (USA: Nevada) and compared to related taxa. This is the first record of the genus in the Western Hemisphere; other species live in the deserts of central Asia. Stackelberginia Lehr is proposed as the sister taxon to Lasiopogon Loew in the subfamily Stichopogoninae based on morphological characters and a Bayesian species tree estimated from one mitochondrial (COI) and three nuclear protein-coding loci (AATS, PEPCK, wingless). Stackelberginia has the medially divided epandrium and rotated hypopygium of Lasiopogon, but the facial gibbosity is flat, macrosetae of thorax, head, and legs are unusually long, and phenology peaks in late autumn. 

scholarly journals The mitochondrial genome and phylogenetic characteristics of the Thick-billed Green-Pigeon, Treron curvirostra: the first sequence for the genus

ZooKeys ◽  
2021 ◽  
Vol 1041 ◽  
pp. 167-182
Author(s):  
Nan Xu ◽  
Jiayu Ding ◽  
Ziting Que ◽  
Wei Xu ◽  
Wentao Ye ◽  
...  
Keyword(s):  
Information System ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Close Relationship ◽  
D Loop ◽  
The Common

Members of the genus Treron (Columbidae) are widely distributed in southern Asia and the Indo-Malayan Region but their relationships are poorly understood. Better knowledge of the systematic status of this genus may help studies of historical biogeography and taxonomy. The complete mitochondrial genome of T. curvirostra was characterized, a first for the genus. It is 17,414 base pairs in length, containing two rRNAs, 22 tRNAs, 13 protein coding genes (PCGs), and one D-loop with a primary structure that is similar to that found in most members of Columbidae. Most PCGs start with the common ATG codon but are terminated by different codons. The highest value of the Ka/Ks ratio within 13 PCGs was found in ATP8 with 0.1937, suggesting that PCGs of the mitochondrial genome tend to be conservative in Columbidae. Moreover, the phylogenetic relationships within Columbidae, which was based on sequences of 13 PCGs, showed that (T. curvirostra + Hemiphaga novaeseelandiae) were clustered in one clade, suggesting a potentially close relationship between Treron and Hemiphaga. However, the monophyly of the subfamilies of Columbidae recognized by the Interagency Taxonomic Information System could not be corroborated. Hence, the position of the genus Treron in the classification of Columbidae may have to be revised.

scholarly journals Identification of the expressome by machine learning on omics data

2019 ◽  
Vol 116 (36) ◽  
pp. 18119-18125 ◽  
Author(s):  
Ryan C. Sartor ◽  
Jaclyn Noshay ◽  
Nathan M. Springer ◽  
Steven P. Briggs
Keyword(s):  
Machine Learning ◽  
Dna Methylation ◽  
Inbred Lines ◽  
Training Data ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Methylation Patterns

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes.

The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes

2007 ◽  
Vol 330 (2) ◽  
pp. 182-187 ◽  
Author(s):  
Nicolas Vidal ◽  
Anne-Sophie Delmas ◽  
Patrick David ◽  
Corinne Cruaud ◽  
Arnaud Couloux ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals First Description of the Mitogenome and Phylogeny of Culicinae Species from the Amazon Region

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1983
Author(s):  
Bruna Laís Sena do Nascimento ◽  
Fábio Silva da Silva ◽  
Joaquim Pinto Nunes-Neto ◽  
Daniele Barbosa de Almeida Medeiros ◽  
Ana Cecília Ribeiro Cruz ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Dna Sequences ◽  
Stop Codon ◽  
Average Length ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Poor ◽  
Aedes Fluviatilis

The Culicidae family is distributed worldwide and comprises about 3587 species subdivided into the subfamilies Anophelinae and Culicinae. This is the first description of complete mitochondrial DNA sequences from Aedes fluviatilis, Aedeomyia squamipennis, Coquillettidia nigricans, Psorophora albipes, and Psorophora ferox. The mitogenomes showed an average length of 15,046 pb and 78.02% AT content, comprising 37 functional subunits (13 protein coding genes, 22 tRNAs, and two rRNAs). The most common start codons were ATT/ATG, and TAA was the stop codon for all PCGs. The tRNAs had the typical leaf clover structure, except tRNASer1. Phylogeny was inferred by analyzing the 13 PCGs concatenated nucleotide sequences of 48 mitogenomes. Maximum likelihood and Bayesian inference analysis placed Ps. albipes and Ps. ferox in the Janthinosoma group, like the accepted classification of Psorophora genus. Ae. fluviatilis was placed in the Aedini tribe, but was revealed to be more related to the Haemagogus genus, a result that may have been hampered by the poor sampling of Aedes sequences. Cq. nigricans clustered with Cq. chrysonotum, both related to Mansonia. Ae. squamipennis was placed as the most external lineage of the Culicinae subfamily. The yielded topology supports the concept of monophyly of all groups and ratifies the current taxonomic classification.

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