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Sequencing and phylogenetic analysis of chloroplast genes in freshwater raphidophytes

Sassenhagen, Ingrid LU and Rengefors, Karin LU (2019) In Genes 10(3).
Abstract

The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, the plastid genomes of the freshwater species Gonyostomum semen and Vacuolaria virescens were sequenced. To exclusively sequence the organelle genomes, chloroplasts were manually isolated and amplified using single-cell whole-genome-amplification. Assembled and annotated chloroplast genes of the two species were phylogenetically compared to the marine raphidophyte Heterosigma akashiwo and other evolutionarily more... (More)

The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, the plastid genomes of the freshwater species Gonyostomum semen and Vacuolaria virescens were sequenced. To exclusively sequence the organelle genomes, chloroplasts were manually isolated and amplified using single-cell whole-genome-amplification. Assembled and annotated chloroplast genes of the two species were phylogenetically compared to the marine raphidophyte Heterosigma akashiwo and other evolutionarily more diverse microalgae. These phylogenetic comparisons confirmed the high relatedness of all investigated raphidophyte species despite their large differences in pigment composition. Notable differences regarding the presence of light-independent protochlorophyllide oxidoreductase (LIPOR) genes among raphidophyte algae were also revealed in this study. The whole-genome amplification approach proved to be useful for isolation of chloroplast DNA from nuclear DNA. Although only approximately 50% of the genomes were covered, this was sufficient for a multiple gene phylogeny representing large parts of the chloroplast genes.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Chloroplast genome, LIPOR, Phylogeny, Raphidophytes, Whole-genome-amplification
in
Genes
volume
10
issue
3
publisher
MDPI AG
external identifiers
  • scopus:85064698029
ISSN
2073-4425
DOI
10.3390/genes10030245
language
English
LU publication?
yes
id
f90f16d8-be53-4fb9-b81e-dfd7dc9ab884
date added to LUP
2019-05-06 10:16:03
date last changed
2019-05-28 03:57:39
@article{f90f16d8-be53-4fb9-b81e-dfd7dc9ab884,
  abstract     = {<p>The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, the plastid genomes of the freshwater species Gonyostomum semen and Vacuolaria virescens were sequenced. To exclusively sequence the organelle genomes, chloroplasts were manually isolated and amplified using single-cell whole-genome-amplification. Assembled and annotated chloroplast genes of the two species were phylogenetically compared to the marine raphidophyte Heterosigma akashiwo and other evolutionarily more diverse microalgae. These phylogenetic comparisons confirmed the high relatedness of all investigated raphidophyte species despite their large differences in pigment composition. Notable differences regarding the presence of light-independent protochlorophyllide oxidoreductase (LIPOR) genes among raphidophyte algae were also revealed in this study. The whole-genome amplification approach proved to be useful for isolation of chloroplast DNA from nuclear DNA. Although only approximately 50% of the genomes were covered, this was sufficient for a multiple gene phylogeny representing large parts of the chloroplast genes.</p>},
  articleno    = {245},
  author       = {Sassenhagen, Ingrid and Rengefors, Karin},
  issn         = {2073-4425},
  keyword      = {Chloroplast genome,LIPOR,Phylogeny,Raphidophytes,Whole-genome-amplification},
  language     = {eng},
  month        = {03},
  number       = {3},
  publisher    = {MDPI AG},
  series       = {Genes},
  title        = {Sequencing and phylogenetic analysis of chloroplast genes in freshwater raphidophytes},
  url          = {http://dx.doi.org/10.3390/genes10030245},
  volume       = {10},
  year         = {2019},
}