Phylogenetic Tree of DNA Sequences Constructed by a New Method-H Curve

The phylogenetic relationship of eight Iris species (I.flavisimma, I.ventricosa, I.bungei,I.kaempferi, I.tenuifolia, I.lactea, I.tigrida, I.dichotoma) were studied by PCR using six specificprimers (S-523, Z1204R, trnL, trnF and ITS1, ITS4). All species except I.ventricosa wereidentified when using S-523, Z1204R and trnL, trnF primers and the DNA fragment size rangedbetween 500 to 600 bp and 800 bp, respectively. Primers ITS1 and ITS4 produced double bandsin about 500 and 1500 bp to I.bungei, I.kaempferi, and I.lactea species. On the phylogenetic tree, some iris species have close relations based on chloroplastic DNA sequences. The closest relationships showed between I.sanguinea and I.sibirica, I.rutenica and I.uniflora. Also I.tenuifolia, I.ventricosa and I.halophila located on one branch of phylogenetic tree.

Download Full-text

Phylogenetic Tree Construction for DNA Sequences using Clustering Methods

Procedia Engineering ◽

10.1016/j.proeng.2012.06.169 ◽

2012 ◽

Vol 38 ◽

pp. 1362-1366 ◽

Cited By ~ 2

Author(s):

Gayatri Mahapatro ◽

Debahuti Mishra ◽

Kailash Shaw ◽

Sashikala Mishra ◽

Tanushree Jena

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences ◽

Clustering Methods ◽

Phylogenetic Tree Construction ◽

Tree Construction

Download Full-text

A new method to analyze the similarity of the DNA sequences

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2007.12.003 ◽

2008 ◽

Vol 853 (1-3) ◽

pp. 62-67 ◽

Cited By ~ 15

Author(s):

Ying Guo ◽

Tian-ming Wang

Keyword(s):

Dna Sequences ◽

New Method

Download Full-text

Reconstruction of Phylogenetic Tree for COX with DNA Sequences

Lecture Notes in Electrical Engineering - Energy Systems, Drives and Automations ◽

10.1007/978-981-15-5089-8_36 ◽

2020 ◽

pp. 369-375

Author(s):

D. Anurag ◽

Chukka Santhaiah ◽

N. V. Krishna Rao ◽

V. JaswanthSai ◽

P. Akash ◽

...

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences

Download Full-text

More on manipulating text.

Practical R for biologists: an introduction ◽

10.1079/9781789245349.0257 ◽

2021 ◽

pp. 257-274

Author(s):

Donald L. J. Quicke ◽

Buntika A. Butcher ◽

Rachel A. Kruft Welton

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences ◽

White Spaces ◽

Using Data ◽

Unknown Length

Abstract This chapter provides more information on manipulating text, presenting two examples. Example 1 focuses on standardizing names in a phylogenetic tree description, using R to reformat taxon names, create lists, sort data and use wildcards for when some things you are interested in don't have exactly the same length. The example tree description concerns parasitoids of caterpillars at a study site that have been DNA barcoded and their possible taxonomic identities added automatically. Example 2 deals with substrings of unknown length. This example search for a numeric substring of unknown length but with a standard prefix, using data of some DNA sequences from a set of Aleiodes wasps. The trimming of white spaces and/or tabs, use of wildcards to locate internal letter strings, finding of suffixes, prefixes and specifying of letters, numbers and punctuation, manipulation of character case, ignoring of character case, and specifying of particular and modifiable character classes are briefly described.

Download Full-text

Strelitziana sarbhoyi sp. nov. (Strelitzianaceae, Chaetothyriales), from North-Western Himalayas, India, described based on morphology and molecular phylogeny

Phytotaxa ◽

10.11646/phytotaxa.427.1.6 ◽

2019 ◽

Vol 427 (1) ◽

pp. 51-59

Author(s):

SHIWALI RANA ◽

SANJAY KUMAR SINGH ◽

PARAS NATH SINGH

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Culture Collection ◽

Fungal Culture ◽

Western Himalayas ◽

Holotype Specimen ◽

North Western

Strelitziana sarbhoyi is established as a new species to accommodate a phylloplane fungus isolated from Mallotus philippensis collected from Kangra region of North-Western Himalayas, Himachal Pradesh. The identity of the fungus is confirmed based on the asexual-morphs, cultural characteristics and phylogenetic analyses of the internal transcribed spacer (ITS) rDNA and partial nuclear ribosomal 28S large subunit (LSU) sequence data. The placement of S. sarbhoyi in the phylogenetic tree was determined based on DNA sequences from authenticated isolates of Strelitziana. Strelitziana sarbhoyi shows nearly 94% similarity with other known species of Strelitziana. Area description is provided for the proposed taxon along with microscopic images, and a phylogenetic tree. This is probably the first report of Strelitziana from India. Holotype specimen (dried voucher culture) is deposited in the Ajrekar Mycological Herbarium (AMH), and an ex-type culture is deposited in National Fungal Culture Collection of India (NFCCI).

Download Full-text