Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) by using sequence variations of an intron and two intergenic spacers of chloroplast DNA

2000 ◽  
Vol 13 (5) ◽  
pp. 745 ◽  
Author(s):  
Daniel J. Murphy ◽  
Frank Udovicic ◽  
Pauline Y. Ladiges
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Small Sample Size ◽  
Intergenic Spacer ◽  
Small Sample ◽  
Total Evidence ◽  
Trnl Intron ◽  
Intergenic Spacers ◽  
Sequence Variations ◽  
Jackknife Support

Three regions of chloroplast DNA are assessed for their utility for phylogenetic analysis of Acacia subgenus Phyllodineae: psbA–trnH intergenic spacer, the trnL intron and the trnL–trnF intergenic spacer. There are large differences in the lengths of the psbA–trnH spacer (155–440 bp) and trnL–trnF intergenic spacer (101–422 bp) regions, and large multi-residue indels were coded as multistate characters. Overall information content in these regions is relatively low, but the total evidence tree has 12 nodes resolved, five with jackknife support. By using Parkia timoriana as the outgroup, Acacia subgenus Acacia (A. farnesiana) is basal and Acacia subgenus Aculeiferum (A. senegal) is the sister taxon to subgenus Phyllodineae. Although based on a small sample size, within subgenus Phyllodineae, the results of this study have shown that section Alatae is not monophyletic, section Lycopodiifoliae is monophyletic and Botrycephalae is related to members of section Phyllodineae with racemose inflorescences.

A reassessment of tribal affinities of the enigmatic genera Printzia and Isoetopsis (Asteraceae), based on three chloroplast sequences

2002 ◽  
Vol 50 (6) ◽  
pp. 677 ◽  
Author(s):  
Randall J. Bayer ◽  
Edward W. Cross
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Trnl Intron ◽  
Coding Region ◽  
Strong Affinity ◽  
Taxonomic History ◽  
Chloroplast Dna Sequences ◽  
Chemical Characters

The tribal affinities of two dubiously placed genera of the Asteraceae, Printzia and Isoetopsis, were assessed by using three chloroplast DNA sequences, the trnL/F spacer, the trnL intron and the matK coding region. The outgroup was represented by two species of the tribe Barnadesieae, whereas one to six genera (43 species including Printzia and Isoetopsis) of the tribes of the Asteroideae [Anthemideae (six genera), Astereae (five) Calenduleae (two), Gnaphalieae (six), Heliantheae s.l. (five), Inuleae s.str. (three), Plucheeae (two), Senecioneae (four)] and Cichorioideae [Arctotideae (one), Cardueae (two), Lactuceae (two), Liabeae (one), Mutisieae (one), Vernonieae (one)] were chosen as the ingroup. Phylogenetic analysis indicates that both Printzia and Isoetopsis have a strong affinity with members of the tribe Astereae. At some point in their taxonomic history, both genera had been placed in this tribe and there are good morphological and chemical characters that justify this placement.

scholarly journals The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
John C. Tracey ◽  
Maricela Coronado ◽  
Tobias W. Giessen ◽  
Maggie C. Y. Lau ◽  
Pamela A. Silver ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Sample Size ◽  
Small Sample Size ◽  
Small Sample ◽  
Anammox Bacteria ◽  
Freshwater Species ◽  
Cargo Protein

AbstractMany prokaryotes encode protein-based encapsulin nanocompartments, including anaerobic ammonium oxidizing (anammox) bacteria. This study expands the list of known anammox encapsulin systems from freshwater species to include the marine genus Scalindua. Two novel systems, identified in “Candidatus Scalindua rubra” and “Candidatus Scalindua sp. SCAELEC01 167” possess different architectures than previously studied freshwater anammox encapsulins. Characterization of the S. rubra encapsulin confirms that it can self-assemble to form compartments when heterologously expressed in Escherichia coli. BLASTp and HMMER searches of additional genomes and metagenomes spanning a range of environments returned 26 additional novel encapsulins, including a freshwater anammox encapsulin identified in “Candidatus Brocadia caroliniensis”. Phylogenetic analysis comparing these 28 new encapsulin sequences and cargo to that of their closest known relatives shows that encapsulins cluster by cargo protein type and therefore likely evolved together. Lastly, prokaryotic encapsulins may be more common and diverse than previously thought. Through searching a small sample size of all public metagenomes and genomes, many new encapsulin systems were unearthed by this study. This suggests that many additional encapsulins likely remain to be discovered.

scholarly journals Genetic Analysis of the Atrial Natriuretic Peptide Gene Polymorphisms among Essential Hypertensive Patients in Malaysia

2016 ◽  
Vol 2016 ◽  
pp. 1-8
Author(s):  
Nooshin Ghodsian ◽  
Patimah Ismail ◽  
Salma Ahmadloo ◽  
Narges Eskandarian ◽  
Ali Etemad
Keyword(s):  
Atrial Natriuretic Peptide ◽  
Natriuretic Peptide ◽  
Gene Polymorphisms ◽  
Small Sample Size ◽  
Sociodemographic Factors ◽  
Small Sample ◽  
Sequence Variations ◽  
Peptide Gene ◽  
Atrial Natriuretic

Background. Atrial natriuretic peptide (ANP) considerably influences blood pressure regulation through water and sodium homoeostasis. Several of the studies have utilized anonymous genetic polymorphic markers and made inconsequent claims about theANPrelevant disorders. Thus, we screened Insertion/Deletion (ID) and G191A polymorphisms ofANPto discover sequence variations with potential functional significance and to specify the linkage disequilibrium pattern between polymorphisms. The relationships of detected polymorphisms with EH with or without Type 2 Diabetes Mellitus (T2DM) status were tested subsequently.Method.ANPgene polymorphisms (I/DandA191G) were specified utilizing mutagenically separated Polymerase Chain Reaction (PCR) in 320 subjects including 163 EH case subjects and 157 controls.Result. This case-control study discovered a significant association betweenI/Dpolymorphisms ofANPgene in EH patient without T2DM. However, the study determined no association between G191A polymorphisms ofANPin EH with or without T2DM. In addition, sociodemographic factors in the case and healthy subjects exhibited strong differences (P<0.05).Conclusion. As a risk factor,ANPgene polymorphisms may affect hypertension. Despite the small sample size in this study, it is the first research assessing theANPgene polymorphisms in both EH and T2DM patients among Malaysian population.

scholarly journals Molecular-phylogenetic analysis of the Cystopteridaceae family from North Asia based on plastid DNA loci

2020 ◽  
Author(s):  
D.O. Ulko ◽  
◽  
I.I. Gureyeva ◽  
R.S. Romanets ◽  
A.A. Kuznetsov ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Intergenic Spacer ◽  
Plastid Dna ◽  
Monotypic Genus ◽  
Phylogenetic Studies ◽  
North Asia ◽  
Matk Gene ◽  
Molecular Phylogenetic ◽  
Gymnocarpium Dryopteris

The results of molecular phylogenetic studies based on the sequencing of matK gene and trnG-R intergenic spacer of the chloroplast DNA and analysis of the concatenated data of these loci of North Asian representatives of the Cystopteridaceae family are presented. In the genus Gymnocarpium, a dryopteris-clade was distinguished including species without glandular pubescence of fronds – Gymnocarpium dryopteris. Species having glandular pubescent fronds have formed the robertianum-clade (G. robertianum and G. fedtschenkoanum), and 2 subclades, including G. continentale, G. jessoense, and G. tenuipes. In the genus Cystopteris, the analysis confirmed the separation of C. montana from other Cystopteris species, and the separation of C. sudetica from the C. fragilis-complex. This advocate the recognition of monotypic genus Rhizomatopteris including Rh. montana (≡Cystopteris montana), and allows to recognize the section Khokhrjakovia (with C. sudetica) within the genus Cystopteris. This analysis did not allow to separate the species of the type subgenus Cystopteris (C. fragilis-complex) from each other.

scholarly journals Lineage analysis of human papillomavirus type 39 in cervical samples of Iranian women

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Neda Hosseini ◽  
Zabihollah Shoja ◽  
Arash Arashkia ◽  
Amir-Hossein Khodadadi ◽  
Somayeh Jalilvand
Keyword(s):  
Sample Size ◽  
Small Sample Size ◽  
Small Sample ◽  
Long Control Region ◽  
E6 Gene ◽  
Sequence Variations ◽  
Geographical Regions ◽  
Hpv Types ◽  
Almost All ◽  
Larger Sample

Abstract Background The data with regards to the regional variants of distinct HPV types is of great value. Accordance with this, this study aimed to investigate the sequence variations of E6 gene and long control region of HPV 39 among normal, premalignant and malignant cervical samples in order to characterize the frequent HPV 39 variants circulating in Tehran, Iran. Methods In total, 70 cervical samples (45 normal, 16 premalignant, and 9 malignant samples) infected with HPV 39 were analyzed by nested-PCR and sequencing. Results Our results revealed that all samples belonged to A lineage. Almost all sequences (98.6%) were classified in A1 sublineage and only one sample (1.4%) was A2 sub lineage. Conclusions Our findings showed that lineages A, sublineage A1, is dominant in Tehran, Iran. However, the small sample size was the most important limitations of this study. Further studies with larger sample size from different geographical regions of Iran are necessary to estimate the pathogenicity risk of HPV 39 variants in this population.

Chloroplast DNA analysis in Tunisian fig cultivars (Ficus carica L.): Sequence variations of the trnL-trnF intergenic spacer

2008 ◽  
Vol 36 (11) ◽  
pp. 828-835 ◽  
Author(s):  
Ghada Baraket ◽  
Saddoud Olfa ◽  
Chatti Khaled ◽  
Mars Messaoud ◽  
Marrakchi Mohamed ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Analysis ◽  
Intergenic Spacer ◽  
Ficus Carica ◽  
Sequence Variations
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