A novice’s guide to analyzing NGS-derived organelle and metagenome data

Song, Hae Jung; Lee, JunMo; Graf, Louis; Rho, Mina; Qiu, Huan; Bhattacharya, Debashish; Yoon, Hwan Su

doi:10.4490/algae.2016.31.6.5

Cited by 18 publications

(14 citation statements)

References 98 publications

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“…Finalized genome maps were created with OGdraw v1.2 49 . The methods used to construct organellar genomes using NGS-derived data generally followed those used by Song et al 50 .…”

Section: Methodsmentioning

confidence: 99%

Organelle inheritance and genome architecture variation in isogamous brown algae

Choi

Graf

Peters

et al. 2020

Sci Rep

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Among the brown algal lineages, ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. in contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. it has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. in contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. to investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDnA) and two mitochondrial genomes (mtDnA) of isogamous species from the ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDnAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDnAs of oogamous species showed no rearrangements. our analysis permits the hypothesis that structural rearrangements in ptDnAs may be a consequence of the mode of inheritance. The brown algae (Phaeophyceae) are a group of photosynthetic heterokonts (=stramenopiles), a secondary endosymbiotic lineage containing red algal-derived plastids 1. The four brown algal orders analyzed in this study, Ectocarpales, Fucales, Laminariales, and Dictyotales, have macroscopic thalli and are distributed worldwide in low-to-mid latitudes where they play important roles in marine ecosystems. Also, they have great potential for commercial uses such as food or in other seaweed industries. From a taxonomic point of view, the orders Ectocarpales, Fucales and Laminariales are grouped into the subclass Fucophycidae, which is defined as a lineage derived from the brown algal crown radiation (BACR), whereas Dictyotales is classified into the Dictyotophycidae 2 (Fig. S1). The life cycles of most brown algae, including species of the Laminariales and Ectocarpales, are characterized by an alternation between a diploid sporophyte and a haploid gametophyte (i.e., a diploid-haploid life cycle). In contrast, in the Fucales meiosis occurs in the parental diploid plants and they directly produce gametes (i.e., a diplontic life cycle) 3,4. Three fertilization types can be defined based on the morphologies and flagella of gametes, independent of whether they are produced via a gametophyte stage or not: the isogamous type in which flagellated gametes are morphologically similar; the anisogamous type where one flagellated gamete is larger than the other; and the oogamous type in which one gamete is a non-motile cell called the egg cell (or oocyte) and the other is a smaller, flagellated sperm cell 5. Most brown algae, including the Laminariales and most species of the Fucales, are oogamous. Anisogamy is only observed in a few lineages such as the Onslowiales, Asterocladales, Nemodermatales, and in some Fucales, Sphacelariales and Ectocarpales species. With the exception of the orders Ecto...

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“…Finalized genome maps were created with OGdraw v1.2 49 . The methods used to construct organellar genomes using NGS-derived data generally followed those used by Song et al 50 .…”

Section: Methodsmentioning

confidence: 99%

Organelle inheritance and genome architecture variation in isogamous brown algae

Choi

Graf

Peters

et al. 2020

Sci Rep

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“…For a comprehensive list of freely available assembly and read mapping programs please refer to Table 2 in Song et al (2016).…”

Section: Box 3: Bioinformatics For Species Delimitationmentioning

confidence: 99%

“…In recent years, high-throughput sequencing (HTS) has become more accessible and this technology has the ability to generate very large data sets at a reasonable cost (e.g., Song et al, 2016). New HTS techniques along with improvements in algorithms for handling/analysing HTS data and falling costs have allowed the development of a wide range of applications and led to a huge increase in molecular sequence data (Reuter et al, 2015;Mardis, 2017).…”

Section: Introductionmentioning

confidence: 99%

High-throughput sequencing for algal systematics

Oliveira

Repetti

Iha

et al. 2018

European Journal of Phycology

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In recent years, the use of molecular data in algal systematics has increased as high-throughput sequencing (HTS) has become more accessible, generating very large data sets at a reasonable cost. In this perspectives paper, our goal is to describe how HTS technologies can advance algal systematics. Following an introduction to some common HTS technologies, we discuss how metabarcoding can accelerate algal species discovery. We show how various HTS methods can be applied to generate datasets for accurate species delimitation, and how HTS can be applied to historical type specimens to assist the nomenclature process. Finally, we discuss how HTS data such as organellar genomes and transcriptomes can be used to construct well resolved phylogenies, leading to a stable and natural classification of algal groups. We include examples of bioinformatic workflows that may be applied to process data for each purpose, along with common programs used to achieve each step. We also discuss possible strategies and the new skill set that will be required to fully embrace HTS as a part of algal systematics, along with considerations of cost and experimental design. HTS technology has revolutionized many fields in biology, and will certainly do the same in algal systematics.

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“…, Song et al. ). The chloroplast, a cyanobacteria‐derived cellular organelle found in diverse photosynthetic eukaryotes, generally contains a circular genome with two inverted repeats (IRs; Turmel et al.…”

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confidence: 99%

Flip‐flop organization in the chloroplast genome of Capsosiphon fulvescens (Ulvophyceae, Chlorophyta)

Kim

Lee

Choi

et al. 2018

Journal of Phycology

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To better understand organelle genome evolution of the ulvophycean green alga Capsosiphon fulvescens, we sequenced and characterized its complete chloroplast genome. The circular chloroplast genome was 111,561 bp in length with 31.3% GC content that contained 108 genes including 77 protein‐coding genes, two copies of rRNA operons, and 27 tRNAs. In this analysis, we found the two types of isoform, called heteroplasmy, were likely caused by a flip‐flop organization. The flip‐flop mechanism may have caused structural variation and gene conversion in the chloroplast genome of C. fulvescens. In a phylogenetic analysis based on all available ulvophycean chloroplast genome data, including a new C. fulvescens genome, we found three major conflicting signals for C. fulvescens and its sister taxon Pseudoneochloris marina within 70 individual genes: (i) monophyly with Ulotrichales, (ii) monophyly with Ulvales, and (iii) monophyly with the clade of Ulotrichales and Ulvales. Although the 70‐gene concatenated phylogeny supported monophyly with Ulvales for both species, these complex phylogenetic signals of individual genes need further investigations using a data‐rich approach (i.e., organelle genome data) from broader taxon sampling.

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A novice’s guide to analyzing NGS-derived organelle and metagenome data

Cited by 18 publications

References 98 publications

Organelle inheritance and genome architecture variation in isogamous brown algae

Organelle inheritance and genome architecture variation in isogamous brown algae

High-throughput sequencing for algal systematics

Flip‐flop organization in the chloroplast genome of Capsosiphon fulvescens (Ulvophyceae, Chlorophyta)

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