scholarly journals Analysis of Phylogenetic Relationships in The Walnut Family Based on Internal Transcribed Spacer Sequences and Secondary Structures(ITS2)

2021 ◽  
Author(s):  
Zhongzhong Guo ◽  
Qiang Jin ◽  
Zhenkun Zhao ◽  
Wenjun Yu ◽  
Gen Li ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Fruit Trees ◽  
Secondary Structures ◽  
Neighbor Joining ◽  
Folding Pattern ◽  
Close Relationship ◽  
Internal Transcribed Spacer Sequences ◽  
Family Based

Abstract This study aims to investigate the phylogenetic relationships within the Juglandaceae family based on the Internal Transcribed Spacer's primary sequence and secondary structures (ITS2). Comparative analysis of 51 Juglandaceae species was performed across most of the defined seven genera. The results showed that the ITS2 secondary structure's folding pattern was highly conserved and congruent with the eukaryote model. Firstly, Neighbor-joining (N.J.) analysis recognized two subfamilies: Platycaryoideae and Engelhardioideae. The Platycaryoideae included the Platycaryeae (Platycarya+(Carya+ Annamocarya)) and Juglandeae (Juglans-(Cyclocarya + Pterocarya)). The Engelhardioideae composed the (Engelhardia+（Oreomunnea+Alfaroa)). The Rhoiptelea genus was generally regarded as an outgroup when inferring the phylogeny of Juglandaceae. However, it is clustered into the Juglandaceae family and showed a close relationship with the Platycaryoideae subfamily. Secondly, the folded 3-helices and 4-helices secondary structure of ITS2 were founded in the Juglandaceae family. Therefore, these ITS2 structures could be used as formal evidence to analyze Juglandaceae's phylogeny relationship. The morphology based on the secondary structure nicely coincided with previous investigations. This study further confirms that ITS2 can serve as a valid basis for parsing evolutionary relationships in higher woody fruit trees.

scholarly journals An ITS-based phylogenetic framework for the genus Vorticella : finding the molecular and morphological gaps in a taxonomically difficult group

2013 ◽  
Vol 280 (1771) ◽  
pp. 20131177 ◽  
Author(s):  
Ping Sun ◽  
John C. Clamp ◽  
Dapeng Xu ◽  
Bangqin Huang ◽  
Mann Kyoon Shin ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Branching Order ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene are too highly conserved to be helpful. In this paper, we move molecular systematics for this group of ciliates to the infrageneric level by sequencing additional molecular markers—fast-evolving internal transcribed spacer (ITS) regions—in a broad sample of 66 individual samples of 28 morphospecies of Vorticella collected from Asia, North America and Europe. Our phylogenies all featured two strongly supported, highly divergent, paraphyletic clades (I, II) comprising the morphologically defined genus Vorticella . Three major lineages made up clade I, with a relatively well-resolved branching order in each one. The marked divergence of clade II from clade I confirms that the former should be recognized as a separate taxonomic unit as indicated by SSU rRNA phylogenies. We made the first attempt to elucidate relationships between species in clade II using both morphological and multi-gene approaches, and our data supported a close relationship between some morphospecies of Vorticella and Opisthonecta , indicating that relationships between species in the clade are far more complex than would be expected from their morphology. Different patterns of helix III of ITS2 secondary structure were clearly specific to clades and subclades of Vorticella and, therefore, may prove useful for resolving phylogenetic relationships in other groups of ciliates.

Phylogenetic relationships of species in Pseudoroegneria (Poaceae: Triticeae) and related genera inferred from nuclear rDNA ITS (internal transcribed spacer) sequences

Biologia ◽  
2008 ◽  
Vol 63 (4) ◽  
Author(s):  
Haiqing Yu ◽  
Xing Fan ◽  
Chun Zhang ◽  
Chunbang Ding ◽  
Xiaoli Wang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
New Genus ◽  
The Other ◽  
Its Sequences ◽  
Agropyron Cristatum ◽  
Tetraploid Species ◽  
Nuclear Rdna ◽  
Rdna Its ◽  
Internal Transcribed Spacer Sequences

AbstractTo evaluate the phylogenetic relationships of species in Pseudoroegneria and related genera, the nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for eighteen Pseudoroegneria (St), two Elytrigia (E e St), two Douglasdeweya (StP), three Lophopyrum (E e and E b), three Agropyron (P), two Hordeum (H), two Australopyrum (W) and two Psathyrostachys (Ns) accessions. The main results were: (i) Pseudoroegneria gracillima, P. stipifolia, P. cognata and P. strigosa (2x) were in one clade, while P. libanotica, P. tauri and P. spicata (2x) were in the other clade, indicating there are the differentiations of St genome among diploid Pseudoroegneria species; (ii) P. geniculata ssp. scythica, P. geniculata ssp. pruinifera, Elytriga caespitosa and Et. caespitosa ssp. nodosa formed the E e St clade with 6-bp indel in ITS1 regions; and (iii) Douglasdeweya wangii, D. deweyi, Agropyron cristatum and A. puberulum comprised the P clade. It is unreasonable to treat P. geniculata ssp. scythica and P. geniculata ssp. pruinifera as the subspecies of P. geniculata, and they should be transferred to a new genus Trichopyrum, which consists of species with E e St genomes. It is also suggested that one of the diploid donor of D. wangii and D. deweyi is derived from Agropyron species, and it is reasonable to treat tetraploid species with StP genomes into Douglasdeweya.

Placozoa: at least two

Biologia ◽  
2007 ◽  
Vol 62 (6) ◽  
Author(s):  
Matthias Wolf ◽  
Christian Selig ◽  
Tobias Müller ◽  
Nicole Philippi ◽  
Thomas Dandekar ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Internal Transcribed Spacer ◽  
Distinct Species ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Structure Alignment ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Internal Transcribed Spacer 2 ◽  
Compensatory Base Changes

AbstractIt was shown that compensatory base changes (CBCs) in internal transcribed spacer 2 (ITS2) sequence-structure alignments can be used for distinguishing species. Using the ITS2 Database in combination with 4SALE — a tool for synchronous RNA sequence and secondary structure alignment and editing — in this study we present an in-depth CBC analysis for placozoan ITS2 sequences and their respective secondary structures. This analysis indicates at least two distinct species in Trichoplax (Placozoa) supporting a recently suggested hypothesis, that Placozoa is “no longer a phylum of one”.

An updated estimate of intergeneric phylogenetic relationships in the Australian VitaceaeThis article is one of a selection of papers presented at the symposium on Vitis at the XVII International Botanical Congress held in Vienna, Austria, in 2005.

2007 ◽  
Vol 85 (8) ◽  
pp. 722-730 ◽  
Author(s):  
Maurizio Rossetto ◽  
Darren M. Crayn ◽  
Betsy R. Jackes ◽  
Carolyn Porter
Keyword(s):  
Internal Transcribed Spacer ◽  
Sister Relationship ◽  
Future Studies ◽  
Australian Species ◽  
International Botanical ◽  
International Botanical Congress ◽  
Close Relationship ◽  
Internal Transcribed Spacer Sequences ◽  
Nuclear Loci ◽  
Selection Of

Previous molecular studies have suggested that the genus Cissus (Vitaceae) is not monophyletic. The majority of species are grouped, but four Australian taxa ( Cissus antarctica Vent., Cissus hypoglauca A. Gray, Cissus oblonga (Benth.) Planch., and Cissus sterculiifolia (F. Muell. ex Benth.) Planch.) form a distinct clade and Cissus opaca has now been recognized as belonging to the genus Clematicissus ( Clematicissus opaca (F. Muell.) Jackes & Rossetto). Here, we investigate relationships among the Australian Vitaceae by parsimony and Bayesian analysis of plastid trnL-trnF and nuclear internal transcribed spacer sequences and include a range of taxa that had not been previously investigated. We find no support for a close relationship between Nothocissus and the four distinct Australian Cissus, as suggested in previous morphology-based treatments. We find a robust sister relationship between Clematicissus and at least two southern American Cissus ( Cissus tweediana (Baker) Planch. and Cissus striata Ruiz & Pav.), suggesting a possible origin from an ancient southern progenitor. Finally, this study confirms the paraphyletic nature of Cayratia , with species occurring in two clades, both with Australian and non-Australian species. The necessity in future studies for data from additional and more tractable nuclear loci is also noted.

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