MEGA: A Bio Computational Software for Sequence and Phylogenetic Analysis

Lecture Notes in Engineering and Computer Science 01/2009;
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Available from: Apurba Dey, Oct 05, 2015
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    • "Phylogenetic trees were constructed with the neighbor-joining algorithm using the program with MEGA 4 ( [49]. Hydrophilicity plots for TcOPT3 was generated based on the Kyte and Doolittle (1982) method using Protean sequence analysis software (DNASTAR) under default parameters. "
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    ABSTRACT: Thlaspi caerulescens is a natural selected heavy metal hyperaccumulator that can not only tolerate but also accumulate extremely high levels of heavy metals in the shoots. Thus, to identify the transportors involved in metal long-distance transportation is very important for understanding the mechanism of heavy metal accumulation in this hyperaccumulator. We cloned and characterized a novel gene TcOPT3 of OPT family from T. caerulescens. TcOPT3 was pronouncedly expressed in aerial parts, including stem and leaf. Moreover, in situ hybridization analyses showed that TcOPT3 expressed in the plant vascular systems, especially in the pericycle cells that may be involved in the long-distance transportation. The expression of TcOPT3 was highly induced by iron (Fe) and zinc (Zn) deficiency, especially in the stem and leaf. Sub-cellular localization showed that TcOPT3 was a plasma membrane-localized protein. Furthermore, heterogonous expression of TcOPT3 by mutant yeast (Saccharomyces cerevisiae) complementation experiments demonstrated that TcOPT3 could transport Fe(2+) and Zn(2+). Moreover, expression of TcOPT3 in yeast increased metal (Fe, Zn, Cu and Cd) accumulation and resulted in an increased sensitivity to cadmium (Cd) and copper (Cu). Our data demonstrated that TcOPT3 might encode an Fe/Zn/Cd/Cu influx transporter with broad-substrate. This is the first report showing that TcOPT3 may be involved in metal long-distance transportation and contribute to the heavy metal hyperaccumulation.
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    ABSTRACT: The annual swarming of epitokes of the eunicid polychaete Palola viridis has great cultural significance in Samoa and other Indo-Pacific locations. Palola spp. occur worldwide in warm shallow-water environments, but not all populations appear to swarm. Morphological distinctions among Palola species are subtle but, based on phylogenetic analysis of mitochondrial markers, two species groups can be distinguished, each containing numerous subclades. The objectives of this study were to determine the position of P. viridis in the phylogeny of the genus, to assess the species’ genetic distinctness and to describe P. viridis epitokes morphologically. We sequenced epitokes from Samoa (locally known as palolo) and Vanuatu (un) for two mitochondrial markers and performed phylogenetic analyses in combination with previously published sequences. The samples from Samoa and Vanuatu formed a common clade in species group B. We suggest that swarming is restricted to this species group, although probably not to a single species.
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