When Less is More: Red Algae as Models for Studying Gene Loss and Genome Evolution in Eukaryotes

Bhattacharya, Debashish,Qiu, Huan,Lee, JunMo,Su Yoon, Hwan,Weber, Andreas P. M.,Price, Dana C. Informa UK (TaylorFrancis) 2018 Critical reviews in plant sciences Vol.37 No.1

Phylogenomics and its Growing Impact on Algal Phylogeny and Evolution

윤환수,Adrian, Reyes-Prieto,Yoon, Hwan-Su,Bhattacharya, Debashish 한국조류학회(藻類) 2006 ALGAE Vol.21 No.1

Genomic data is accumulating in public database at an unprecedented rate. Although presently dominated by the sequences of metazoan, plant, parasitic, and picoeukaryotic taxa, both expressed sequence tag (EST) and complete genomes of free-living algae are also slowly appearing. This wealth of information offers the opportunity to clarify many long-standing issues in algal and plant evolution such as the contribution of the plastid endosymbiont to nuclear genome evolution using the tools of comparative genomics and multi-gene phylogenetics. A particularly powerful approach for the automated analysis of genome data from multiple taxa is termed phylogenomics. Phylogenomics is the convergence of genomics science (the study of the function and structure of genes and genomes) and molecular phylogenetics (the study of the hierarchical evolutionary relationships among organisms, their genes and genomes). The use of phylogenetics to drive comparative genome analyses has facilitated the reconstruction of the evolutionary history of genes, gene families, and organisms. Here we survey the available genome data, introduce phylogenomic pipelines, and review some initial results of phylogenomic analyses of algal genome data.

Ancient gene paralogy may mislead inference of plastid phylogeny.

Qiu, Huan,Yang, Eun Chan,Bhattacharya, Debashish,Yoon, Hwan Su University of Chicago Press 2012 Molecular biology and evolution Vol.29 No.11

<P>Because of its ancient origin more than 1 billion years ago, the highly reduced plastid genomes of Plantae (e.g., plant chloroplasts) provide limited insights into the initial stages of endosymbiont genome reduction. The photosynthetic amoeba Paulinella provides a more useful model to study this process because its alpha-cyanobacterium-derived plastid originated 60 Ma and the genome still contains 1,000 genes. Here, we compared and contrasted features associated with genome reduction due to primary endosymbiosis in Paulinella plastids and in marine, free-living strains of the picocyanobacterium, Prochlorococcus. Both types of genomes show gene inactivation, concerted evolution, and contraction of gene families that impact highly conserved single-copy phylogenetic markers in the plastid such as psbA, psbC, and psbD. Our data suggest that these photosystem II genes may provide misleading phylogenetic signal because each of the constituent Plantae lineages has likely undergone a different, independent series of events that led to their reduction to a single copy. This issue is most problematic for resolving basal Plantae relationships when differential plastid gene loss was presumably ongoing, as we observe in Paulinella species. Our work uncovers a key, previously unappreciated aspect of organelle genome reduction and demonstrates 'work-in-progress' models such as Paulinella to be critical to gain a fuller understanding of algal and plant genome evolution.</P>

Applications of next-generation sequencing to unravelling the evolutionary history of algae

Kim, Kyeong Mi,Park, Jun-Hyung,Bhattacharya, Debashish,Yoon, Hwan Su International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.2

<P>First-generation Sanger DNA sequencing revolutionized science over the past three decades and the current next-generation sequencing (NGS) technology has opened the doors to the next phase in the sequencing revolution. Using NGS, scientists are able to sequence entire genomes and to generate extensive transcriptome data from diverse photosynthetic eukaryotes in a timely and cost-effective manner. Genome data in particular shed light on the complicated evolutionary history of algae that form the basis of the food chain in many environments. In the Eukaryotic Tree of Life, the fact that photosynthetic lineages are positioned in four supergroups has important evolutionary consequences. We now know that the story of eukaryotic photosynthesis unfolds with a primary endosymbiosis between an ancestral heterotrophic protist and a captured cyanobacterium that gave rise to the glaucophytes, red algae and Viridiplantae (green algae and land plants). These primary plastids were then transferred to other eukaryotic groups through secondary endosymbiosis. A red alga was captured by the ancestor(s) of the stramenopiles, alveolates (dinoflagellates, apicomplexa, chromeridae), cryptophytes and haptophytes, whereas green algae were captured independently by the common ancestors of the euglenophytes and chlorarachniophytes. A separate case of primary endosymbiosis is found in the filose amoeba <I>Paulinella chromatophora</I>, which has at least nine heterotrophic sister species. <I>Paulinella</I> genome data provide detailed insights into the early stages of plastid establishment. Therefore, genome data produced by NGS have provided many novel insights into the taxonomy, phylogeny and evolutionary history of photosynthetic eukaryotes.</P>

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

송해중,이준모,Louis Graf,노미나,Huan Qiu,Debashish Bhattacharya,윤환수 한국조류학회I 2016 ALGAE Vol.31 No.2

Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to thesharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genomedata sets is however still a challenging task because it often requires significant computer resources andknowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGSdata. We focus specifically on the analysis of organelle genome and metagenome data and describe the currentbioinformatic pipelines suited for this purpose.

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 The Korean Society of Phycology 2016 ALGAE Vol.31 No.2

Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to the sharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genome data sets is however still a challenging task because it often requires significant computer resources and knowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGS data. We focus specifically on the analysis of organelle genome and metagenome data and describe the current bioinformatic pipelines suited for this purpose.

The Algal Revolution

Brodie, Juliet,Chan, Cheong Xin,De Clerck, Olivier,Cock, J. Mark,Coelho, Susana M.,Gachon, Claire,Grossman, Arthur R.,Mock, Thomas,Raven, John A.,Smith, Alison G.,Yoon, Hwan Su,Bhattacharya, Debashish Elsevier 2017 Trends in plant science Vol.22 No.8

<P>Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput ‘omic’ and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.</P> <P><B>Trends</B></P> <P>Application of modern ‘omic and genetic methods has significantly advanced our understanding of the origin, evolution, and metabolic potential of unicellular and multicellular algae, as well as their diverse modes of sexual reproduction.</P> <P>The GreenCut proteins, a conserved gene set in the Viridiplantae, are primarily plastid targeted and have key roles in the function and regulation of photosynthesis, including the maintenance of photosynthetic reaction complexes.</P> <P>Lab evolution experiments demonstrate the strong adaptability of microalgae to environmental changes that are associated with climate change, although it is unclear whether these results will hold in natural ecosystems.</P> <P>The development of algae as ‘cell factories’ promises to allow the production of not only endogenous molecules, but also non-native compounds such as high-value pigments, bulk chemicals, or even therapeutic proteins.</P>

Complex phylogeographic patterns in the freshwater alga <i>Synura</i> provide new insights into ubiquity vs. endemism in microbial eukaryotes

BOO, SUNG MIN,KIM, HAN SOON,SHIN, WOONGGHI,BOO, GA HUN,CHO, SUNG MI,JO, BOK YEON,KIM, JEE-HWAN,KIM, JIN HEE,YANG, EUN CHAN,SIVER, PETER A.,WOLFE, ALEXANDER P.,BHATTACHARYA, DEBASHISH,ANDERSEN, ROBERT Blackwell Publishing Ltd 2010 Molecular ecology Vol.19 No.19

<P>Abstract</P><P>The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multigene data set, we study the phylogeography of the freshwater heterokont alga <I>Synura petersenii sensu lato</I>. Our results suggest that this <I>Synura</I> morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus <I>Synura</I> is considerably older than currently proposed. The availability of tectonically relevant geological time (10<SUP>7</SUP>–10<SUP>8</SUP> years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explains global patterns of microbial eukaryote distribution and that processes of dispersal remain poorly understood.</P>