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{{Short description|Family of protozoans}}
{{more citations needed|date=March 2015}}
{{Taxobox
{{Taxobox
| image = Diplonema papillatum SEM image.gif
| image_alt = Scanning electron micrograph of "Diplonema papillatum"
| image_caption = [[Scanning electron micrograph]] of ''[[Diplonema papillatum]]''
| domain = [[Eukaryota]]
| domain = [[Eukaryota]]
| unranked_regnum = [[Excavata]]
| unranked_regnum = [[Excavata]]
| phylum = [[Euglenozoa]]
| phylum = [[Euglenozoa]]
| classis = Diplonemea
| classis = [[Diplonemea]]
| ordo = Diplonemida
| ordo = [[Diplonemida]]
| familia = '''Diplonemidae'''
| familia = '''Diplonemidae'''
| familia_authority = Cavalier-Smith 1993
| familia_authority = Cavalier-Smith 1993 emend. Adl et al. 2019
| subdivision_ranks = Genus
| subdivision_ranks = Genus
| subdivision =
| subdivision =
* ''[[Diplonema (genus)|Diplonema]]'' <small>Griessmann 1913 non Don 1837</small>
* ''[[Diplonema (excavate)|Diplonema]]''
* ''[[Rhynchopus]]'' <small>Skuja 1948</small>
* ''[[Flectonema]]''
* ''[[Lacrimia]]''
⚫
* ''[[Rhynchopus]]''
* ''[[Sulcionema]]''
| synonyms =
| synonyms =
* Rhynchopodaceae <small>Skuja 1948 ex Cavalier-Smith 1993</small>
* Rhynchopodaceae <small>Skuja 1948 ex Cavalier-Smith 1993</small>
}}
}}


'''Diplonemidae''' is a biflagellated unicellular protist of the diplnemida order, and is potentially the most diverse and common planktonic organism in the ocean. Although this family is currently made up of three named genera; ''[[Diplonema (excavate)|Diplonema]]'', ''Rhynchopus'', and ''[[Hemistasia]]'', there still exists thousands of unnamed genera.<ref name=":0">{{Cite journal|last=Flegontova|first=Olga|last2=Flegontov|first2=Pavel|last3=Malviya|first3=Shruti|last4=Audic|first4=Stephane|last5=Wincker|first5=Patrick|last6=Vargas|first6=Colomban de|last7=Bowler|first7=Chris|last8=Lukeš|first8=Julius|last9=Horák|first9=Aleš|title=Extreme Diversity of Diplonemid Eukaryotes in the Ocean|url=http://linkinghub.elsevier.com/retrieve/pii/S096098221631082X|journal=Current Biology|volume=26|issue=22|pages=3060–3065|doi=10.1016/j.cub.2016.09.031}}</ref> Organisms are generally colourless and oblong in shape, with two flagella emerging from a subapical pocket.<ref name=":1">{{Cite journal|last=Gawryluk|first=Ryan M.R.|last2=Campo|first2=Javier del|last3=Okamoto|first3=Noriko|last4=Strassert|first4=Jürgen F.H.|last5=Lukeš|first5=Julius|last6=Richards|first6=Thomas A.|last7=Worden|first7=Alexandra Z.|last8=Santoro|first8=Alyson E.|last9=Keeling|first9=Patrick J.|title=Morphological Identification and Single-Cell Genomics of Marine Diplonemids|url=http://linkinghub.elsevier.com/retrieve/pii/S0960982216310624|journal=Current Biology|volume=26|issue=22|pages=3053–3059|doi=10.1016/j.cub.2016.09.013}}</ref> They possess a large mitochondrial genome composed of fragmented linear DNA <ref name=":2">{{Cite journal|last=Lukeš|first=Julius|last2=Flegontova|first2=Olga|last3=Horák|first3=Aleš|title=Diplonemids|url=http://linkinghub.elsevier.com/retrieve/pii/S0960982215005035|journal=Current Biology|volume=25|issue=16|pages=R702–R704|doi=10.1016/j.cub.2015.04.052}}</ref> These non-coding sequences must be massively trans-spliced, making it one of the most complicated post-transcriptional editing process known to eukaryotes.
'''Diplonemidae''' is a family of biflagellated unicellular protists that may be among the more diverse and common groups of planktonic organisms in the ocean. Although this family is currently made up of three named genera; ''[[Diplonema (excavate)|Diplonema]]'', ''[[Rhynchopus]]'', and ''[[Hemistasia]]'', there likely exist thousands of still unnamed genera.<ref name=pmid27875689>{{cite journal |doi=10.1016/j.cub.2016.09.031 |pmid=27875689 |title=Extreme Diversity of Diplonemid Eukaryotes in the Ocean |journal=Current Biology |volume=26 |issue=22 |pages=3060–3065 |year=2016 |last1=Flegontova |first1=Olga |last2=Flegontov |first2=Pavel |last3=Malviya |first3=Shruti |last4=Audic |first4=Stephane |last5=Wincker |first5=Patrick |last6=De Vargas |first6=Colomban |last7=Bowler |first7=Chris |last8=Lukeš |first8=Julius |last9=Horák |first9=Aleš |doi-access=free }}</ref> Organisms are generally colourless and oblong in shape, with two flagella emerging from a subapical pocket.<ref name=pmid27875688>{{cite journal |doi=10.1016/j.cub.2016.09.013 |pmid=27875688 |title=Morphological Identification and Single-Cell Genomics of Marine Diplonemids |journal=Current Biology |volume=26 |issue=22 |pages=3053–3059 |year=2016 |last1=Gawryluk |first1=Ryan M.R. |last2=Del Campo |first2=Javier |last3=Okamoto |first3=Noriko |last4=Strassert |first4=Jürgen F.H. |last5=Lukeš |first5=Julius |last6=Richards |first6=Thomas A. |last7=Worden |first7=Alexandra Z. |last8=Santoro |first8=Alyson E. |last9=Keeling |first9=Patrick J. |doi-access=free }}</ref> They possess a large mitochondrial genome composed of fragmented linear DNA. <ref name=pmid26294177>{{cite journal |doi=10.1016/j.cub.2015.04.052 |pmid=26294177 |title=Diplonemids |journal=Current Biology |volume=25 |issue=16 |pages=R702–R704 |year=2015 |last1=Lukeš |first1=Julius |last2=Flegontova |first2=Olga |last3=Horák |first3=Aleš |doi-access=free }}</ref> These non-coding sequences must be massively trans-spliced, making it one of the most complicated post-transcriptional editing process known to eukaryotes.


==Etymology==
==Etymology==
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== History of Knowledge ==
== History of Knowledge ==
Primary studies done in the 1900s by Griessmann and Skuja had initially grouped Diplonemidae (or more specifically, the ''[[Diplonema (excavate)|Diplonema]]'' and ''Rhynchopus'' taxa) with the euglenids. This was due to the two groups sharing many morphological similarities with the [[euglenid]]s, such as metaboly, locomotion and a microtubule-reinforced feeding apparatus.<ref name=":3">{{Cite journal|last=ROY|first=JOANNIE|last2=FAKTOROVÁ|first2=DRAHOMÍRA|last3=BENADA|first3=OLDŘICH|last4=LUKEŠ|first4=JULIUS|last5=BURGER|first5=GERTRAUD|date=2007-03-01|title=Description of Rhynchopus euleeides n. sp. (Diplonemea), a Free-Living Marine Euglenozoan|url=http://doi.wiley.com/10.1111/j.1550-7408.2007.00244.x|journal=The Journal of Eukaryotic Microbiology|language=en|volume=54|issue=2|pages=137–145|doi=10.1111/j.1550-7408.2007.00244.x|issn=1550-7408}}</ref> However, this conclusion was met with some controversy, as diplonemids lacked characteristic features shared by all euglenids, such as possession of pellicle strips and paraxonemal rods on their flagella.<ref name=":4">{{Cite journal|last=HEYDEN|first=SOPHIE|last2=CHAO|first2=EMA E.|last3=VICKERMAN|first3=KEITH|last4=CAVALIER-SMITH|first4=THOMAS|date=2004-07-01|title=Ribosomal RNA Phylogeny of Bodonid and Diplonemid Flagellates and the Evolution of Euglenozoa|url=http://doi.wiley.com/10.1111/j.1550-7408.2004.tb00387.x|journal=The Journal of Eukaryotic Microbiology|language=en|volume=51|issue=4|pages=402–416|doi=10.1111/j.1550-7408.2004.tb00387.x|issn=1550-7408}}</ref> Instead, they were placed in the euglenozoan phylum and shared this taxon with the kinetoplastids and euglenids.<ref name=":5">{{Cite journal|last=Simpson|first=Alastair G.B.|title=The identity and composition of the Euglenozoa|url=http://linkinghub.elsevier.com/retrieve/pii/S0003936597800127|journal=Archiv für Protistenkunde|volume=148|issue=3|pages=318–328|doi=10.1016/s0003-9365(97)80012-7}}</ref> The inclusion of ''Rhynchopus'' and ''Diplonema'' in the family Diplonemidae was later confirmed through nuclear 18S rRNA analysis.<ref>{{Cite journal|last=Busse|first=I|last2=Preisfeld|first2=Angelika|title=Phylogenetic position of Rhynchopus sp. and Diplonema ambulator as indicated by analyses of euglenozoan small subunit ribosomal DNA|url=http://linkinghub.elsevier.com/retrieve/pii/S0378111902003906|journal=Gene|volume=284|issue=1-2|pages=83–91|doi=10.1016/s0378-1119(02)00390-6}}</ref> As of now, ''Rhynchopus'' and ''diplonema'' are part of the ‘classical’ diplonemidae subgroup, whilst ''hemistasia'' is part of the ‘nonclassical’ diplonemidae subgroup.
Primary studies done in the 1900s by Griessmann and Skuja had initially grouped Diplonemidae (or more specifically, the ''[[Diplonema (excavate)|Diplonema]]'' and ''Rhynchopus'' taxa) with the euglenids. This was due to the two groups sharing many morphological similarities with the [[euglenid]]s, such as metaboly, locomotion and a microtubule-reinforced feeding apparatus.<ref name=pmid17403154>{{cite journal |doi=10.1111/j.1550-7408.2007.00244.x |pmid=17403154 |title=Description of ''Rhynchopus euleeides'' n. sp. (Diplonemea), a Free-Living Marine Euglenozoan |journal=The Journal of Eukaryotic Microbiology |volume=54 |issue=2 |pages=137–145 |year=2007 |last1=Roy |first1=Joannie |last2=Faktorová |first2=Drahomíra |last3=Benada |first3=Oldřich |last4=Lukeš |first4=Julius |last5=Burger |first5=Gertraud }}</ref> However, this conclusion was met with some controversy, as diplonemids lacked characteristic features shared by all euglenids, such as possession of pellicle strips and paraxonemal rods on their flagella.<ref name="Heyden et al 2004">{{cite journal |doi=10.1111/j.1550-7408.2004.tb00387.x |title=Ribosomal RNA Phylogeny of Bodonid and Diplonemid Flagellates and the Evolution of Euglenozoa |journal=The Journal of Eukaryotic Microbiology |volume=51 |issue=4 |pages=402–416 |year=2004 |last1=Heyden |first1=Sophie |last2=Chao |first2=EMA E. |last3=Vickerman |first3=Keith |last4=Cavalier-Smith |first4=Thomas }}</ref> Instead, they were placed in the euglenozoan phylum and shared this taxon with the kinetoplastids and euglenids.<ref name=Simpson1997>{{cite journal |doi=10.1016/s0003-9365(97)80012-7 |title=The identity and composition of the Euglenozoa |journal=Archiv für Protistenkunde |volume=148 |issue=3 |pages=318–328 |year=1997 |last1=Simpson |first1=Alastair G.B. }}</ref> The inclusion of ''Rhynchopus'' and ''Diplonema'' in the family Diplonemidae was later confirmed through nuclear 18S rRNA analysis.<ref name=pmid11891049>{{cite journal |doi=10.1016/s0378-1119(02)00390-6 |pmid=11891049 |title=Phylogenetic position of ''Rhynchopus'' sp. and ''Diplonema ambulator'' as indicated by analyses of euglenozoan small subunit ribosomal DNA |journal=Gene |volume=284 |issue=1–2 |pages=83–91 |year=2002 |last1=Busse |first1=I. |last2=Preisfeld |first2=Angelika }}</ref> As of now, ''Rhynchopus'' and ''Diplonema'' are part of the ‘classical’ diplonemid subgroup, and ''Hemistasia'' is part of the ‘nonclassical’ diplonemid subgroup.


Recently, there had been debates as to whether Diplonemidae were more closely related to the [[euglenid]]s or [[Kinetoplastida|kinetoplastids]]. It was not until analysis of cytosolic heat shock proteins that a sister relationship between the diplonemids and kinetoplastids was proposed.<ref name=":4" /> This was further supported through phylogenetic analysis, which discovered that diplonemidae possess a functional splice leader RNA that is characteristic of the kinetoplastids.<ref>{{Cite journal|last=STURM|first=NANCY R.|last2=MASLOV|first2=DMITRI A.|last3=GRISARD|first3=EDMUNDO C.|last4=CAMPBELL|first4=DAVID A.|date=2001-05-01|title=Diplonema spp. Possess Spliced Leader RNA Genes Similar to the Kinetoplastida|url=http://doi.wiley.com/10.1111/j.1550-7408.2001.tb00321.x|journal=The Journal of Eukaryotic Microbiology|language=en|volume=48|issue=3|pages=325–331|doi=10.1111/j.1550-7408.2001.tb00321.x|issn=1550-7408}}</ref> Additionally, the amino acid tryptophan is encoded by codon TGA in kinetoplastids and diplonemids, whereas in euglenids, the regular codon is used instead.<ref name=":4" />  
Recently, there had been debates as to whether Diplonemidae were more closely related to the [[Euglenidae|euglenids]] or [[Kinetoplastida|kinetoplastids]]. It was not until analysis of cytosolic heat shock proteins that a sister relationship between the diplonemids and kinetoplastids was proposed.<ref name="Heyden et al 2004"/> This was further supported through phylogenetic analysis, which discovered that Diplonemidae possess a functional splice leader RNA that is characteristic of the kinetoplastids.<ref>{{cite journal |doi=10.1111/j.1550-7408.2001.tb00321.x |title=''Diplonema'' spp. Possess Spliced Leader RNA Genes Similar to the Kinetoplastida |journal=The Journal of Eukaryotic Microbiology |volume=48 |issue=3 |pages=325–331 |year=2001 |last1=Sturm |first1=Nancy R. |last2=Maslov |first2=Dmitri A. |last3=Grisard |first3=Edmundo C. |last4=Campbell |first4=David A. }}</ref> Additionally, the amino acid tryptophan is encoded by codon TGA in kinetoplastids and diplonemids, whereas in euglenids, the regular codon is used instead.<ref name="Heyden et al 2004"/>


Nevertheless, despite the similarities between kinetoplastids and diplonemids, the two taxa are still distinct form each other. Diplonemidae still lack a kinetoplast, and have a unique bi-flagellated trophic phase not seen in kinetoplastids. Presently, the kinetoplastids are regarded as the sister group to the Diplonemidae.
Nevertheless, despite the similarities between kinetoplastids and diplonemids, the two taxa are still distinct form each other. Diplonemidae still lack a kinetoplast, and have a unique bi-flagellated trophic phase not seen in kinetoplastids. Presently, the kinetoplastids are regarded as the sister group to the Diplonemidae.


Although there are only three named genera within the Diplonemidae, environmental sequencing performed by the recent TARA Ocean Expedition concluded there are potentially thousands of genera,<ref name=":0" /> suggesting that pelagic Diplonemidae are the most diverse planktonic eukaryotes in the oceans.
Although there are only three named genera within the Diplonemidae, environmental sequencing performed by the recent TARA Ocean Expedition concluded there are potentially thousands of genera,<ref name=pmid27875689/> suggesting that pelagic Diplonemidae are the most diverse planktonic eukaryotes in the oceans.


== Habitat and Ecology ==
== Habitat and Ecology ==
Although Diplonemidae are generally predators, some species display parasitic life strategies.<ref name=":2" /> Diplonemidae display a rich diversity in marine and freshwater environments, with their relative abundance increasing with depth.<ref>{{Cite journal|last=Debroas|first=Didier|last2=Domaizon|first2=Isabelle|last3=Humbert|first3=Jean-Francois|last4=Jardillier|first4=Ludwig|last5=Lepère|first5=Cécile|last6=Oudart|first6=Anne|last7=Taïb|first7=Najwa|date=2017-04-01|title=Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data|url=https://academic.oup.com/femsec/article/93/4/fix023/3059202|journal=FEMS Microbiology Ecology|language=en|volume=93|issue=4|doi=10.1093/femsec/fix023|issn=0168-6496}}</ref> The diplonemids that exist in these different environments are genetically distinct, and exhibit slightly different lifestyles. The ‘classic’ diplonemids (i.e. ''Diplonema'' and ''Rhynchopus'') are benthic, whereas the marine diplonemids, which include ''Hemistasia'', are planktonic.<ref name=":1" /> 
Although Diplonemidae are generally predators, some species display parasitic life strategies.<ref name=pmid26294177/> Diplonemidae display a rich diversity in marine and freshwater environments, with their relative abundance increasing with depth.<ref name=pmid28334157>{{cite journal |doi=10.1093/femsec/fix023 |pmid=28334157 |title=Overview of freshwater microbial eukaryotes diversity: A first analysis of publicly available metabarcoding data |journal=FEMS Microbiology Ecology |volume=93 |issue=4 |year=2017 |last1=Debroas |first1=Didier |last2=Domaizon |first2=Isabelle |last3=Humbert |first3=Jean-Francois |last4=Jardillier |first4=Ludwig |last5=Lepère |first5=Cécile |last6=Oudart |first6=Anne |last7=Taïb |first7=Najwa |doi-access=free }}</ref> The diplonemids that exist in these different environments are genetically distinct, and exhibit slightly different lifestyles. The ‘classic’ diplonemids (i.e. ''Diplonema'' and ''Rhynchopus'') are benthic, whereas the marine diplonemids, which include ''Hemistasia'', are planktonic.<ref name=pmid27875688/>


There are potentially thousands of unknown marine Diplonemidae species, with this diversity highly stratified in accordance to depth. Although molecular sequencing confirms the existence of these unnamed marine Diplonemidae, information regarding their morphology and lifestyle is absent.<ref name=":0" /> As marine ''Diplonemidae'' are the most abundant and genetically diverse protists (and potentially eukaryotes) in the sea, there are strong implications that they play a key role in aquatic ecosystems. As of now, this exact role is unknown.
There are potentially thousands of unknown marine Diplonemidae species, with this diversity highly stratified in accordance to depth. Although molecular sequencing confirms the existence of these unnamed marine Diplonemidae, information regarding their morphology and lifestyle is absent.<ref name=pmid27875689/> As marine Diplonemidae are the most abundant and genetically diverse protists (and potentially eukaryotes) in the sea, there are strong implications that they play a key role in aquatic ecosystems. As of now, this exact role is unknown.


== Description of the Organism ==
== Description of the Organism ==


=== Morphology and Anatomy ===
=== Morphology and Anatomy ===
Classical diplonemids (i.e. ''Diplonema'' and ''Rhynchopus''), are colourless and oblong in shape. They are approximately 20 μm in length and possess a microtubule layer underneath their plasma membrane.<ref name=":6">{{Cite journal|last=Triemer|first=Richard E.|last2=Ott|first2=Donald W.|title=Ultrastructure of Diplonema ambulator larsen & patterson (euglenozoa) and its relationship to Isonema|url=http://linkinghub.elsevier.com/retrieve/pii/S0932473911801239|journal=European Journal of Protistology|volume=25|issue=4|pages=316–320|doi=10.1016/s0932-4739(11)80123-9}}</ref> Adjacent to it is a mitochondrium with discoidal cristae.<ref name=":5" /> They also possess two flagella of equal length, both of which lack paraxial rods.<ref name=":1" /> The two basal bodies originate from a subapical pocket, which merges with an adjacent feeding apparatus.<ref name=":3" /> This feeding apparatus is surrounded by many food vacuoles and reinforced by microtubules.<ref name=":6" />
Classical diplonemids (i.e. ''Diplonema'' and ''Rhynchopus''), are colourless and oblong in shape. They are approximately 20 μm in length and possess a microtubule layer underneath their plasma membrane.<ref name=pmid23196044>{{cite journal |doi=10.1016/s0932-4739(11)80123-9 |pmid=23196044 |title=Ultrastructure of Diplonema ambulator larsen & patterson (euglenozoa) and its relationship to Isonema |journal=European Journal of Protistology |volume=25 |issue=4 |pages=316–320 |year=1990 |last1=Triemer |first1=Richard E. |last2=Ott |first2=Donald W. }}</ref> Adjacent to it is a mitochondrion with discoidal cristae.<ref name=Simpson1997/> They also possess two flagella of equal length, both of which lack paraxial rods.<ref name=pmid27875688/> The two basal bodies originate from a subapical pocket, which merges with an adjacent feeding apparatus.<ref name=pmid17403154/> This feeding apparatus is surrounded by many food vacuoles and reinforced by microtubules.<ref name=pmid23196044/>


Nonclassical ''Diplonemidae'' (i.e. ''Hemistasia)'' are diverse in size but share many morphological aspects with the classic diplonemids. However, a great majority of these marine ''Diplonemidae'' have never been seen, with their existence only confirmed through molecular analysis.<ref name=":1" />
Nonclassical Diplonemidae (i.e. ''Hemistasia)'' are diverse in size but share many morphological aspects with the classic diplonemids. However, a great majority of these marine Diplonemidae have never been seen, with their existence only confirmed through molecular analysis.<ref name=pmid27875688/>


Although ''Diplonemidae'' do not possess pellicular strips like ''Euglenids'', they still move via metaboly.<ref name=":2" />
Although Diplonemidae do not possess pellicular strips like [[Euglenidae|euglenids]], they still move via metaboly.<ref name=pmid26294177/>


''Diplonemidae'' also exhibit the  compartmentalization of glycolytic and gluconeogenic enzymes into peroxisomes. These organelles are referred to as glycosomes, and is a characteristic feature also shared with their sister taxon, the ''[[Linetoplastids]]''.<ref>{{Cite journal|last=Gabaldón|first=Toni|last2=Ginger|first2=Michael L.|last3=Michels|first3=Paul A.M.|title=Peroxisomes in parasitic protists|url=http://linkinghub.elsevier.com/retrieve/pii/S0166685116300135|journal=Molecular and Biochemical Parasitology|volume=209|issue=1-2|pages=35–45|doi=10.1016/j.molbiopara.2016.02.005}}</ref>
Diplonemidae also exhibit the compartmentalization of glycolytic and gluconeogenic enzymes into peroxisomes. These organelles are referred to as glycosomes, and is a characteristic feature also shared with their sister taxon, the ''[[kinetoplastids]]''.<ref name=pmid26896770>{{cite journal |doi=10.1016/j.molbiopara.2016.02.005 |pmid=26896770 |title=Peroxisomes in parasitic protists |journal=Molecular and Biochemical Parasitology |volume=209 |issue=1–2 |pages=35–45 |year=2016 |last1=Gabaldón |first1=Toni |last2=Ginger |first2=Michael L. |last3=Michels |first3=Paul A.M. }}</ref>


=== Life cycles ===
=== Life cycles ===
''Diplonemidae'' are capable of sexual reproduction, as genes involved in meiosis have been found.<ref>{{Cite journal|last=Goodenough|first=Ursula|last2=Heitman|first2=Joseph|date=2014-03-01|title=Origins of Eukaryotic Sexual Reproduction|url=http://cshperspectives.cshlp.org/content/6/3/a016154|journal=Cold Spring Harbor Perspectives in Biology|language=en|volume=6|issue=3|pages=a016154|doi=10.1101/cshperspect.a016154|issn=1943-0264|pmid=24591519|pmc=3949356}}</ref> Although marine diplonemids appear to reproduce sexually, not much is known about ''Diplonemidae'' reproduction as ''[[Euglenozoa]]ns'' rarely demonstrate sexual processes.<ref name=":4" />
Diplonemidae are capable of sexual reproduction, as genes involved in meiosis have been found.<ref name=pmid24591519>{{cite journal |doi=10.1101/cshperspect.a016154 |pmid=24591519 |pmc=3949356 |title=Origins of Eukaryotic Sexual Reproduction |journal=Cold Spring Harbor Perspectives in Biology |volume=6 |issue=3 |pages=a016154 |year=2014 |last1=Goodenough |first1=U. |last2=Heitman |first2=J. }}</ref> Although marine diplonemids appear to reproduce sexually, not much is known about diplonemid reproduction as ''[[Euglenozoa]]ns'' rarely demonstrate sexual processes.<ref name="Heyden et al 2004"/>


=== Genetics ===
=== Genetics ===
''Diplonemidae'' have a very unique mitochondrial DNA arrangement. Although ''Diplonemidae'' possess a large mitochondrial genome, these do not contain any intact full-sized genes. Instead, their mitochondrial DNA consists of linear gene fragments of different sizes. Because each fragment is both full of repeats and incomplete, individually they are unable to code for a gene themselves. Instead, fragments are transcribed and spliced together using their own specialized trans splicing machinery.<ref name=":2" /> Once spliced together, the transcript undergoes extensive editing to become recognizable RNA. This is accomplished by either Uracil-insertion, nucleotide deanimation, or substitution, which eventually generates a fully mature and translatable transcript.<ref>{{Cite journal|last=David|first=Vojtěch|last2=Archibald|first2=John M.|title=Evolution: Plumbing the Depths of Diplonemid Diversity|url=http://linkinghub.elsevier.com/retrieve/pii/S0960982216312787|journal=Current Biology|volume=26|issue=24|pages=R1290–R1292|doi=10.1016/j.cub.2016.10.050}}</ref>
Diplonemidae have a very unique mitochondrial DNA arrangement. Although Diplonemidae possess a large mitochondrial genome, these do not contain any intact full-sized genes. Instead, their mitochondrial DNA consists of linear gene fragments of different sizes. Because each fragment is both full of repeats and incomplete, individually they are unable to code for a gene themselves. Instead, fragments are transcribed and spliced together using their own specialized trans splicing machinery.<ref name=pmid26294177/> Once spliced together, the transcript undergoes extensive editing to become recognizable RNA. This is accomplished by either Uracil-insertion, nucleotide deanimation, or substitution, which eventually generates a fully mature and translatable transcript.<ref name=pmid27997843>{{cite journal |doi=10.1016/j.cub.2016.10.050 |pmid=27997843 |title=Evolution: Plumbing the Depths of Diplonemid Diversity |journal=Current Biology |volume=26 |issue=24 |pages=R1290–R1292 |year=2016 |last1=David |first1=Vojtěch |last2=Archibald |first2=John M. |doi-access=free }}</ref>


The ''Diplonemidae'' genome contains a spliced leader RNA gene, which confirms their use of mRNA spliceosome-dependent trans splicing during nuclear expression.
The Diplonemidae genome contains a spliced leader RNA gene, which confirms their use of mRNA spliceosome-dependent trans splicing during nuclear expression.


Interestingly, diplonemids possess the gap3 gene which is specifically found in [[cyanobacteria]] and [[proteobacteria]]. This is likely due to lateral gene transfer following the divergence of diplonemids from the ''Euglenoids''.<ref>{{Cite journal|last=QIAN|first=Q|title=Diplonemid Glyceraldehyde-3-PhosphateDehydrogenase (GAPDH) and Prokaryote-to-Eukaryote Lateral Gene Transfer|url=http://linkinghub.elsevier.com/retrieve/pii/S1434461004700590|journal=Protist|volume=152|issue=3|pages=193–201|doi=10.1078/1434-4610-00059}}</ref> As to date, this is one of the most-supported examples of lateral gene transfer from a bacterium to eukaryote and may have implications for diplonemid acquisition of biochemical abilities.
Diplonemids possess the ''gap3'' gene which is specifically found in [[cyanobacteria]] and [[Pseudomonadota]]. This is likely due to lateral gene transfer following the divergence of diplonemids from the euglenoids.<ref name=pmid11693658>{{cite journal |doi=10.1078/1434-4610-00059 |pmid=11693658 |title=Diplonemid Glyceraldehyde-3-Phosphate ''Dehydrogenase'' (GAPDH) and Prokaryote-to-Eukaryote Lateral Gene Transfer |journal=Protist |volume=152 |issue=3 |pages=193–201 |year=2001 |last1=Qian |first1=Q. |last2=Keeling |first2=P. J. }}</ref> As to date, this is one of the most-supported examples of lateral gene transfer from a bacterium to eukaryote and may have implications for diplonemid acquisition of biochemical abilities.


== Taxonomy==
== List of Named Species ==
⚫
Although presently made up of less than a dozen named species, the existence of thousands of unknown diplonemid species has been confirmed.<ref name=pmid27875689/>
List of named species


* Genus ''[[Diplonema (excavate)|Diplonema]]'' <small>Griessmann 1913 non Don 1837</small>
⚫
Although presently made up of less than a dozen named species, the existence of thousands of unknown ''Diplonemidae'' species has been confirmed.<ref name=":0" />
** ''[[Diplonema aggregatum|D. aggregatum]]'' <small>Tashyreva et al. 2018</small>

* ''[[Diplonema nigricans]]''<ref name=":6" />
** ''[[Diplonema ambulator|D. ambulator]]'' <small>Larsen & Patterson 1990</small>
* ''[[Diplonema papillatum]]''<ref name=":6" />
** ''[[Diplonema breviciliatum|D. breviciliatum]]'' <small>Griessman 1913</small>
* ''[[Diplonema ambulator]]''
** ''[[Diplonema japonicum|D. japonicum]]'' <small>Tashyreva et al. 2018</small>
* ''[[Diplonema metabolicum]]''
** ''[[Diplonema metabolicum|D. metabolicum]]'' <small>Larsen & Patterson 1990</small>
** ''[[Diplonema nigricans|D. nigricans]]'' <small>(Schuster, Goldstein & Hershenow 1968) Triemer & Ott 1990</small> [''Isonema nigricans'' <small>Schuster, Goldstein & Hershenow 1968</small>]<ref name=pmid23196044/>
* ''[[Diplonema breviciliata]]''
** ''[[Diplonema papillatum|D. papillatum]]'' <small>(Porter 1973) Triemer & Ott 1990</small> [''Isonema papillata'' <small>Porter 1973</small>]<ref name=pmid23196044/>
⚫
* ''[[Rhynchopus euleeides]]'' <ref name=":3" />
* Genus ''[[Flectonema]]'' <small>Tashyreva et al. 2018</small>
⚫
* ''[[Rhynchopus amitus]]''
** ''[[Flectonema neradi|F. neradi]]'' <small>Tashyreva et al. 2018</small>
⚫
* ''[[Rhynchopus coscinodiscivorus]]''
* Genus ''[[Lacrimia]]'' <small>Tashyreva et al. 2018</small>
⚫
* ''[[Rhynchopus littoralensis]]''
** ''[[Lacrimia lanifica|L. lanifica]]'' <small>Tashyreva et al. 2018</small><ref name=pmid29604574/>
* ''[[Hemistasia phaeocysticola]]''
* Genus ''[[Rhynchopus]]'' <small>Skuja 1948</small>
** ''[[Rhynchopus amitus|R. amitus]]'' <small>Skuja 1948</small>
⚫
** ''[[Rhynchopus coscinodiscivorus|R. coscinodiscivorus]]'' <small>Schnepf 1994</small>
⚫
** ''[[Rhynchopus euleeides|R. euleeides]]'' <small>Roy et al. 2007</small><ref name=pmid17403154/>
** ''[[Rhynchopus humris|R. humris]]'' <small>Tashyreva et al. 2018</small>
⚫
** ''[[Rhynchopus littoralensis|R. littoralensis]]'' <small>Kufferath 1950</small>
** ''[[Rhynchopus serpens|R. serpens]]'' <small>Tashyreva et al. 2018</small>
* ''[[Sulcionema]]'' <small>Tashyreva et al. 2018</small><ref name=pmid29604574>{{cite journal |doi=10.1016/j.protis.2018.02.001 |pmid=29604574 |title=Phylogeny and Morphology of New Diplonemids from Japan |journal=Protist |volume=169 |issue=2 |pages=158–179 |year=2018 |last1=Tashyreva |first1=Daria |last2=Prokopchuk |first2=Galina |last3=Yabuki |first3=Akinori |last4=Kaur |first4=Binnypreet |last5=Faktorová |first5=Drahomíra |last6=Votýpka |first6=Jan |last7=Kusaka |first7=Chiho |last8=Fujikura |first8=Katsunori |last9=Shiratori |first9=Takashi |last10=Ishida |first10=Ken-Ichiro |last11=Horák |first11=Aleš |last12=Lukeš |first12=Julius }}</ref>
** ''[[Sulcionema specki|S. specki]]'' <small>Tashyreva et al. 2018</small>


==References==
==References==
{{Reflist}}
{{Reflist}}


{{Eukaryota classification}}
{{Eukaryota classification}}{{Excavata}}
{{Taxonbar|from=Q19760075}}
{{Taxonbar|from=Q8560156}}


[[Category:Euglenozoa]]
[[Category:Euglenozoa]]

Revision as of 23:47, 30 December 2023

Diplonemidae
Scanning electron micrograph of "Diplonema papillatum"
Scanning electron micrograph of Diplonema papillatum
Scientific classification
Domain:
Eukaryota
(unranked):
Excavata
Phylum:
Euglenozoa
Class:
Diplonemea
Order:
Diplonemida
Family:
Diplonemidae

Cavalier-Smith 1993 emend. Adl et al. 2019
Genus
Synonyms
  • Rhynchopodaceae Skuja 1948 ex Cavalier-Smith 1993

Diplonemidae is a family of biflagellated unicellular protists that may be among the more diverse and common groups of planktonic organisms in the ocean. Although this family is currently made up of three named genera; Diplonema, Rhynchopus, and Hemistasia, there likely exist thousands of still unnamed genera.[1] Organisms are generally colourless and oblong in shape, with two flagella emerging from a subapical pocket.[2] They possess a large mitochondrial genome composed of fragmented linear DNA. [3] These non-coding sequences must be massively trans-spliced, making it one of the most complicated post-transcriptional editing process known to eukaryotes.

Etymology

The word “Diplonemidae” come from the Greek words ‘diplo’, meaning two, and ‘nemat’, meaning thread. Together, Diplonemidae roughly translates to ‘two threads’, likely referring to the characteristic two flagella of the organism.

History of Knowledge

Primary studies done in the 1900s by Griessmann and Skuja had initially grouped Diplonemidae (or more specifically, the Diplonema and Rhynchopus taxa) with the euglenids. This was due to the two groups sharing many morphological similarities with the euglenids, such as metaboly, locomotion and a microtubule-reinforced feeding apparatus.[4] However, this conclusion was met with some controversy, as diplonemids lacked characteristic features shared by all euglenids, such as possession of pellicle strips and paraxonemal rods on their flagella.[5] Instead, they were placed in the euglenozoan phylum and shared this taxon with the kinetoplastids and euglenids.[6] The inclusion of Rhynchopus and Diplonema in the family Diplonemidae was later confirmed through nuclear 18S rRNA analysis.[7] As of now, Rhynchopus and Diplonema are part of the ‘classical’ diplonemid subgroup, and Hemistasia is part of the ‘nonclassical’ diplonemid subgroup.

Recently, there had been debates as to whether Diplonemidae were more closely related to the euglenids or kinetoplastids. It was not until analysis of cytosolic heat shock proteins that a sister relationship between the diplonemids and kinetoplastids was proposed.[5] This was further supported through phylogenetic analysis, which discovered that Diplonemidae possess a functional splice leader RNA that is characteristic of the kinetoplastids.[8] Additionally, the amino acid tryptophan is encoded by codon TGA in kinetoplastids and diplonemids, whereas in euglenids, the regular codon is used instead.[5]

Nevertheless, despite the similarities between kinetoplastids and diplonemids, the two taxa are still distinct form each other. Diplonemidae still lack a kinetoplast, and have a unique bi-flagellated trophic phase not seen in kinetoplastids. Presently, the kinetoplastids are regarded as the sister group to the Diplonemidae.

Although there are only three named genera within the Diplonemidae, environmental sequencing performed by the recent TARA Ocean Expedition concluded there are potentially thousands of genera,[1] suggesting that pelagic Diplonemidae are the most diverse planktonic eukaryotes in the oceans.

Habitat and Ecology

Although Diplonemidae are generally predators, some species display parasitic life strategies.[3] Diplonemidae display a rich diversity in marine and freshwater environments, with their relative abundance increasing with depth.[9] The diplonemids that exist in these different environments are genetically distinct, and exhibit slightly different lifestyles. The ‘classic’ diplonemids (i.e. Diplonema and Rhynchopus) are benthic, whereas the marine diplonemids, which include Hemistasia, are planktonic.[2]

There are potentially thousands of unknown marine Diplonemidae species, with this diversity highly stratified in accordance to depth. Although molecular sequencing confirms the existence of these unnamed marine Diplonemidae, information regarding their morphology and lifestyle is absent.[1] As marine Diplonemidae are the most abundant and genetically diverse protists (and potentially eukaryotes) in the sea, there are strong implications that they play a key role in aquatic ecosystems. As of now, this exact role is unknown.

Description of the Organism

Morphology and Anatomy

Classical diplonemids (i.e. Diplonema and Rhynchopus), are colourless and oblong in shape. They are approximately 20 μm in length and possess a microtubule layer underneath their plasma membrane.[10] Adjacent to it is a mitochondrion with discoidal cristae.[6] They also possess two flagella of equal length, both of which lack paraxial rods.[2] The two basal bodies originate from a subapical pocket, which merges with an adjacent feeding apparatus.[4] This feeding apparatus is surrounded by many food vacuoles and reinforced by microtubules.[10]

Nonclassical Diplonemidae (i.e. Hemistasia) are diverse in size but share many morphological aspects with the classic diplonemids. However, a great majority of these marine Diplonemidae have never been seen, with their existence only confirmed through molecular analysis.[2]

Although Diplonemidae do not possess pellicular strips like euglenids, they still move via metaboly.[3]

Diplonemidae also exhibit the compartmentalization of glycolytic and gluconeogenic enzymes into peroxisomes. These organelles are referred to as glycosomes, and is a characteristic feature also shared with their sister taxon, the kinetoplastids.[11]

Life cycles

Diplonemidae are capable of sexual reproduction, as genes involved in meiosis have been found.[12] Although marine diplonemids appear to reproduce sexually, not much is known about diplonemid reproduction as Euglenozoans rarely demonstrate sexual processes.[5]

Genetics

Diplonemidae have a very unique mitochondrial DNA arrangement. Although Diplonemidae possess a large mitochondrial genome, these do not contain any intact full-sized genes. Instead, their mitochondrial DNA consists of linear gene fragments of different sizes. Because each fragment is both full of repeats and incomplete, individually they are unable to code for a gene themselves. Instead, fragments are transcribed and spliced together using their own specialized trans splicing machinery.[3] Once spliced together, the transcript undergoes extensive editing to become recognizable RNA. This is accomplished by either Uracil-insertion, nucleotide deanimation, or substitution, which eventually generates a fully mature and translatable transcript.[13]

The Diplonemidae genome contains a spliced leader RNA gene, which confirms their use of mRNA spliceosome-dependent trans splicing during nuclear expression.

Diplonemids possess the gap3 gene which is specifically found in cyanobacteria and Pseudomonadota. This is likely due to lateral gene transfer following the divergence of diplonemids from the euglenoids.[14] As to date, this is one of the most-supported examples of lateral gene transfer from a bacterium to eukaryote and may have implications for diplonemid acquisition of biochemical abilities.

Taxonomy

Although presently made up of less than a dozen named species, the existence of thousands of unknown diplonemid species has been confirmed.[1]

References

  1. ^ a b c d Flegontova, Olga; Flegontov, Pavel; Malviya, Shruti; Audic, Stephane; Wincker, Patrick; De Vargas, Colomban; Bowler, Chris; Lukeš, Julius; Horák, Aleš (2016). "Extreme Diversity of Diplonemid Eukaryotes in the Ocean". Current Biology. 26 (22): 3060–3065. doi:10.1016/j.cub.2016.09.031. PMID 27875689.
  2. ^ a b c d Gawryluk, Ryan M.R.; Del Campo, Javier; Okamoto, Noriko; Strassert, Jürgen F.H.; Lukeš, Julius; Richards, Thomas A.; Worden, Alexandra Z.; Santoro, Alyson E.; Keeling, Patrick J. (2016). "Morphological Identification and Single-Cell Genomics of Marine Diplonemids". Current Biology. 26 (22): 3053–3059. doi:10.1016/j.cub.2016.09.013. PMID 27875688.
  3. ^ a b c d Lukeš, Julius; Flegontova, Olga; Horák, Aleš (2015). "Diplonemids". Current Biology. 25 (16): R702–R704. doi:10.1016/j.cub.2015.04.052. PMID 26294177.
  4. ^ a b c Roy, Joannie; Faktorová, Drahomíra; Benada, Oldřich; Lukeš, Julius; Burger, Gertraud (2007). "Description of Rhynchopus euleeides n. sp. (Diplonemea), a Free-Living Marine Euglenozoan". The Journal of Eukaryotic Microbiology. 54 (2): 137–145. doi:10.1111/j.1550-7408.2007.00244.x. PMID 17403154.
  5. ^ a b c d Heyden, Sophie; Chao, EMA E.; Vickerman, Keith; Cavalier-Smith, Thomas (2004). "Ribosomal RNA Phylogeny of Bodonid and Diplonemid Flagellates and the Evolution of Euglenozoa". The Journal of Eukaryotic Microbiology. 51 (4): 402–416. doi:10.1111/j.1550-7408.2004.tb00387.x.
  6. ^ a b Simpson, Alastair G.B. (1997). "The identity and composition of the Euglenozoa". Archiv für Protistenkunde. 148 (3): 318–328. doi:10.1016/s0003-9365(97)80012-7.
  7. ^ Busse, I.; Preisfeld, Angelika (2002). "Phylogenetic position of Rhynchopus sp. and Diplonema ambulator as indicated by analyses of euglenozoan small subunit ribosomal DNA". Gene. 284 (1–2): 83–91. doi:10.1016/s0378-1119(02)00390-6. PMID 11891049.
  8. ^ Sturm, Nancy R.; Maslov, Dmitri A.; Grisard, Edmundo C.; Campbell, David A. (2001). "Diplonema spp. Possess Spliced Leader RNA Genes Similar to the Kinetoplastida". The Journal of Eukaryotic Microbiology. 48 (3): 325–331. doi:10.1111/j.1550-7408.2001.tb00321.x.
  9. ^ Debroas, Didier; Domaizon, Isabelle; Humbert, Jean-Francois; Jardillier, Ludwig; Lepère, Cécile; Oudart, Anne; Taïb, Najwa (2017). "Overview of freshwater microbial eukaryotes diversity: A first analysis of publicly available metabarcoding data". FEMS Microbiology Ecology. 93 (4). doi:10.1093/femsec/fix023. PMID 28334157.
  10. ^ a b c d Triemer, Richard E.; Ott, Donald W. (1990). "Ultrastructure of Diplonema ambulator larsen & patterson (euglenozoa) and its relationship to Isonema". European Journal of Protistology. 25 (4): 316–320. doi:10.1016/s0932-4739(11)80123-9. PMID 23196044.
  11. ^ Gabaldón, Toni; Ginger, Michael L.; Michels, Paul A.M. (2016). "Peroxisomes in parasitic protists". Molecular and Biochemical Parasitology. 209 (1–2): 35–45. doi:10.1016/j.molbiopara.2016.02.005. PMID 26896770.
  12. ^ Goodenough, U.; Heitman, J. (2014). "Origins of Eukaryotic Sexual Reproduction". Cold Spring Harbor Perspectives in Biology. 6 (3): a016154. doi:10.1101/cshperspect.a016154. PMC 3949356. PMID 24591519.
  13. ^ David, Vojtěch; Archibald, John M. (2016). "Evolution: Plumbing the Depths of Diplonemid Diversity". Current Biology. 26 (24): R1290–R1292. doi:10.1016/j.cub.2016.10.050. PMID 27997843.
  14. ^ Qian, Q.; Keeling, P. J. (2001). "Diplonemid Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) and Prokaryote-to-Eukaryote Lateral Gene Transfer". Protist. 152 (3): 193–201. doi:10.1078/1434-4610-00059. PMID 11693658.
  15. ^ a b Tashyreva, Daria; Prokopchuk, Galina; Yabuki, Akinori; Kaur, Binnypreet; Faktorová, Drahomíra; Votýpka, Jan; Kusaka, Chiho; Fujikura, Katsunori; Shiratori, Takashi; Ishida, Ken-Ichiro; Horák, Aleš; Lukeš, Julius (2018). "Phylogeny and Morphology of New Diplonemids from Japan". Protist. 169 (2): 158–179. doi:10.1016/j.protis.2018.02.001. PMID 29604574.
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