The complete chloroplast genome sequence of Ulva linza
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METHODS AND RESOURCES ARTICLE
The complete chloroplast genome sequence of Ulva linza Lingke Wang1 · Chuner Cai1,2 · Lingjie Zhou1 · Peimin He1 · Binghua Jiao1,2
Received: 26 December 2016 / Accepted: 30 December 2016 © Springer Science+Business Media Dordrecht 2017
Abstract Ulva linza is one of the causal species that result in the macroalgal blooms around Yellow Sea, China. The blooms have now become the world’s largest green tide, making great disaster for the ecosystem. We analyzed whole genome sequence of chloroplast for the first time (GenBank accession number KX058323). It was found that the annular-shape genome was made up of 86,726 bp, including 67 protein coding genes. We then aligned amino acids of chlorophyta species containing 44 common genes in series as phylogenetic tree, which shows Chlorophyceae and Trebouxiophyceae separately cluster except for Leptosiraterrestri. In the phylogenetic tree of amino acid alignment, Ulvophyceae, Pedinophyceae, Prasinophytes and Chlorophyta incertae sedis are independent cluster respectively, and closer to Trebouxiophyceae in the origin. Keywords
Green tides · Chloroplast genome · Ulva linza
Lingke Wang and Chuner Cai have contributed equally to this work. * Peimin He [email protected] * Binghua Jiao [email protected] Lingke Wang [email protected] Chuner Cai [email protected] 1
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
2
Marine Biomedicine Institute, Second Military Medical University, Shanghai, China
Green tide algae Ulva is widely distributed around the world, especially in the sea and estuarial area. They have the ability to fit into adverse situation, and grow rapidly in the eutrophication water area (Tan et al. 1999). Though Ulva species have bad effect for the ecosystem, only two chloroplast whole genome of Ulva species were determined (GenBank accession number NC_029040.1 and KP720617.1). From 2007, the green tides broke out continuously in the Yellow Sea, resulting in great marine environment and ecosystem service functions deterioration (Huo et al. 2013; Liu et al. 2015; Wu et al. 2014). U. linza was identified as the early counterpart that caused green tide breakout (Han et al. 2013). Moreover, the chloroplast DNA of Ulva could be used as molecular markers, playing important role in genetic structure, species identification and phyletic evolution (Melton et al. 2015). U. linza was collected from Rudong sea area in Jiangsu. Segment amplification and adjusted primers were used in chloroplast sequencing of U. linza. Takara LA Taq was employed for amplification with the segments over 4000 bp; Takara Ex Taq for amplification with those below 4000 bp. Long fragment PCR product was interrupt by ultrasonic after electrophoresis test. Then the product was connected to carrier PMD19-T, and trasferred to escherichia coli DH5a. For the positive clones, shotgun sequencing method was employed at ABI3730 sequencer, and the result was joined by the software phred
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