Editing Dinoflagellate (section)

==Genomics==

One of the most striking features of dinoflagellates is the large amount of cellular DNA that they contain. Most eukaryotic algae contain on average about 0.54 pg DNA/cell, whereas estimates of dinoflagellate DNA content range from 3–250 pg/cell,<ref name="Spector" /> corresponding to roughly 3000–215 000 Mb (in comparison, the haploid human genome is 3180 Mb and hexaploid ''Triticum'' wheat is 16 000 Mb). [[Polyploidy]] or polyteny may account for this large cellular DNA content,<ref>{{cite book |first1=Carl A. |last1=Beam |first2=Marion |last2=Himes |title=Ch. 8: Dinoflagellate genetics |url=https://books.google.com/books?id=qCcgFximE8oC&pg=PA263 |pages=263–298 |isbn=978-0-3231-3813-0 |date=2012-12-02 |publisher=Academic Press |access-date=2016-03-05 |archive-date=2014-07-07 |archive-url=https://web.archive.org/web/20140707091932/http://books.google.com/books?id=qCcgFximE8oC&pg=PA263 |url-status=live }} In {{harvnb|Spector|1984}}</ref> but earlier studies of DNA reassociation kinetics and recent genome analyses do not support this hypothesis.<ref>{{cite journal | vauthors = Lin S, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y, Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse D | title = The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis | journal = Science | volume = 350 | issue = 6261 | pages = 691–694 | date = November 2015 | pmid = 26542574 | doi = 10.1126/science.aad0408 | doi-access = free | bibcode = 2015Sci...350..691L }}</ref> Rather, this has been attributed, hypothetically, to the rampant retroposition found in dinoflagellate genomes.<ref>{{cite journal | vauthors = Song B, Morse D, Song Y, Fu Y, Lin X, Wang W, Cheng S, Chen W, Liu X, Lin S | title = Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution | journal = Genome Biology and Evolution | volume = 9 | issue = 8 | pages = 2037–2047 | date = August 2017 | pmid = 28903461 | pmc = 5585692 | doi = 10.1093/gbe/evx144 }}</ref><ref>{{cite journal | vauthors = Hou Y, Ji N, Zhang H, Shi X, Han H, Lin S | title = Genome size-dependent pcna gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism | journal = Journal of Phycology | volume = 55 | issue = 1 | pages = 37–46 | date = February 2019 | pmid = 30468510 | doi = 10.1111/jpy.12815 | doi-access = free | bibcode = 2019JPcgy..55...37H }}</ref>

In addition to their disproportionately large genomes, dinoflagellate nuclei are unique in their morphology, regulation, and composition. Their DNA is so tightly packed that exactly how many chromosomes they have is still uncertain.<ref>{{cite web |author=University of Queensland |date=13 May 2019 |url= https://www.sciencedaily.com/releases/2019/05/190513100546.htm |title=Understanding relationship break-ups to protect the reef |website=ScienceDaily |access-date=16 May 2019 |archive-date=13 May 2019 |archive-url= https://web.archive.org/web/20190513171043/https://www.sciencedaily.com/releases/2019/05/190513100546.htm |url-status=live}}</ref>

The dinoflagellates share an unusual mitochondrial genome organisation with their relatives, the [[Apicomplexa]].<ref name=Jackson2011>{{cite journal | vauthors = Jackson CJ, Gornik SG, Waller RF | title = The mitochondrial genome and transcriptome of the basal dinoflagellate Hematodinium sp.: character evolution within the highly derived mitochondrial genomes of dinoflagellates | journal = Genome Biology and Evolution | volume = 4 | issue = 1 | pages = 59–72 | year = 2012 | pmid = 22113794 | pmc = 3268668 | doi = 10.1093/gbe/evr122 }}</ref> Both groups have very reduced mitochondrial genomes (around 6 kilobases (kb) in the Apicomplexa vs ~16kb for human mitochondria). One species, ''[[Amoebophrya]] ceratii'', has lost its mitochondrial genome completely, yet still has functional mitochondria.<ref>{{cite journal | vauthors = John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G | title = An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome | journal = Science Advances | volume = 5 | issue = 4 | pages = eaav1110 | date = April 2019 | pmid = 31032404 | pmc = 6482013 | doi = 10.1126/sciadv.aav1110 | bibcode = 2019SciA....5.1110J }}</ref> The genes on the dinoflagellate genomes have undergone a number of reorganisations, including massive genome amplification and recombination which have resulted in multiple copies of each gene and gene fragments linked in numerous combinations. Loss of the standard stop codons, trans-splicing of mRNAs for the mRNA of cox3, and extensive RNA editing recoding of most genes has occurred.<ref>{{cite journal | vauthors = Lin S, Zhang H, Spencer DF, Norman JE, Gray MW | title = Widespread and extensive editing of mitochondrial mRNAS in dinoflagellates | journal = Journal of Molecular Biology | volume = 320 | issue = 4 | pages = 727–739 | date = July 2002 | pmid = 12095251 | doi = 10.1016/S0022-2836(02)00468-0 }}</ref><ref>{{cite book | vauthors = Lin S, Zhang H, Gray MW | chapter = RNA editing in dinoflagellates and its implications for the evolutionary history of the editing machinery | publisher = Wiley | editor-last = Smith | editor-first = H. | title = RNA and DNA editing: Molecular Mechanisms and Their Integration into Biological Systems | pages = 280–309 | year = 2008 | chapter-url = {{GBurl|DyFZFqG-d0QC|p=280}} | isbn = 978-0-470-26225-2 }}</ref> The reasons for this transformation are unknown. In a small group of dinoflagellates, called 'dinotoms' (Durinskia and Kryptoperidinium), the endosymbionts (diatoms) still have mitochondria, making them the only organisms with two evolutionarily distinct mitochondria.<ref>{{cite journal | vauthors = Imanian B, Pombert JF, Dorrell RG, Burki F, Keeling PJ | title = Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts | journal = PLOS ONE | volume = 7 | issue = 8 | pages = e43763 | year = 2012 | pmid = 22916303 | pmc = 3423374 | doi = 10.1371/journal.pone.0043763 | bibcode = 2012PLoSO...743763I | doi-access = free }}</ref>

In most of the species, the plastid genome consist of just 14 genes.<ref>{{cite journal|title=Marine parasite survives without key genes|journal = Nature Middle East|doi=10.1038/nmiddleeast.2019.63|year = 2019|last1 = Das|first1 = Biplab|s2cid = 149458671}}</ref>

The DNA of the plastid in the peridinin-containing dinoflagellates is contained in a series of small circles called [[minicircle]]s.<ref name=Laatsch2004>{{cite journal | vauthors = Laatsch T, Zauner S, Stoebe-Maier B, Kowallik KV, Maier UG | title = Plastid-derived single gene minicircles of the dinoflagellate Ceratium horridum are localized in the nucleus | journal = Molecular Biology and Evolution | volume = 21 | issue = 7 | pages = 1318–1322 | date = July 2004 | pmid = 15034134 | doi = 10.1093/molbev/msh127 | doi-access = free }}</ref> Each circle contains one or two polypeptide genes. The genes for these polypeptides are chloroplast-specific because their homologs from other photosynthetic eukaryotes are exclusively encoded in the chloroplast genome. Within each circle is a distinguishable 'core' region. Genes are always in the same orientation with respect to this core region.

In terms of [[DNA barcoding]], ITS sequences can be used to identify species,<ref>{{cite journal | vauthors = Stern RF, Andersen RA, Jameson I, Küpper FC, Coffroth MA, Vaulot D, Le Gall F, Véron B, Brand JJ, Skelton H, Kasai F, Lilly EL, Keeling PJ | title = Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker | journal = PLOS ONE | volume = 7 | issue = 8 | pages = e42780 | year = 2012 | pmid = 22916158 | pmc = 3420951 | doi = 10.1371/journal.pone.0042780 | doi-access = free | bibcode = 2012PLoSO...742780S | author-link5 = Mary Alice Coffroth }}</ref> where a genetic distance of p≥0.04 can be used to delimit species,<ref>{{cite journal |vauthors=Litaker RW, Vandersea MW, Kibler SR, Reece KS, Stokes NA, Lutzoni FM, Yonish BA, West MA, Black MN, Tester PA |title=Recognizing dinoflagellate species using ITS rDNA sequences |journal=J. Phycol. |volume=43 |issue= 2|pages=344–355 |date=April 2007 |doi=10.1111/j.1529-8817.2007.00320.x |bibcode=2007JPcgy..43..344W |s2cid=85929661 }}</ref> which has been successfully applied to resolve long-standing taxonomic confusion as in the case of resolving the Alexandrium tamarense complex into five species.<ref>{{cite journal | vauthors = Wang L, Zhuang Y, Zhang H, Lin X, Lin S | title = DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species | journal = Harmful Algae | volume = 31 | pages = 100–113 | date = January 2014 | pmid = 28040099 | doi = 10.1016/j.hal.2013.10.013 | bibcode = 2014HAlga..31..100W }}</ref> A recent study<ref>{{cite journal | vauthors = Stephens TG, Ragan MA, Bhattacharya D, Chan CX | title = Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions | journal = Scientific Reports | volume = 8 | issue = 1 | pages = 17175 | date = November 2018 | pmid = 30464192 | pmc = 6249206 | doi = 10.1038/s41598-018-35620-z | ref = Stephens2018 | bibcode = 2018NatSR...817175S }}</ref> revealed a substantial proportion of dinoflagellate genes encode for unknown functions, and that these genes could be conserved and lineage-specific.