The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism\u27s genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images of all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclature will assist end users to properly classify genome assemblies, thus facilitating genomic analysis

Graphodatsky, Alexander S.

Lewin, Harris A.

Marshall Graves, Jennifer A.

O\u27Brien, Stephen James

Ryder, Oliver A.

English

NSU Works

Nova Southeastern UniversityNSUWorksBiology Faculty Articles Department of Biological Sciences8-22-2019Precision nomenclature for the new genomicsHarris A. LewinUniversity of California, DavisJennifer A. Marshall GravesLaTrobe University - Melbourne, AustraliaOliver A. RyderSan Diego Zoo Institute for Conservation ResearchAlexander S. GraphodatskyInstitute of Molecular and Cell Biology - Novosibirsk, Russia; Novosibirsk State University - RussiaStephen James O'BrienSt. Petersburg State University; Nova Southeastern University, sobrien1@nova.eduFollow this and additional works at: https://nsuworks.nova.edu/cnso_bio_facarticlesPart of the Biology Commons, and the Genomics CommonsThis Article is brought to you for free and open access by the Department of Biological Sciences at NSUWorks. It has been accepted for inclusion inBiology Faculty Articles by an authorized administrator of NSUWorks. For more information, please contact nsuworks@nova.edu.NSUWorks CitationLewin, Harris A.; Jennifer A. Marshall Graves; Oliver A. Ryder; Alexander S. Graphodatsky; and Stephen James O'Brien. 2019."Precision nomenclature for the new genomics." GigaScience 8, (8): giz086. doi:10.1093/gigascience/giz086.GigaScience, 8, 2019, 1–3doi: 10.1093/gigascience/giz086CommentaryCOMMENTARYPrecision nomenclature for the new genomicsHarris A. Lewin 1,*, Jennifer A. Marshall Graves2, Oliver A. Ryder3,Alexander S. Graphodatsky4,5 and Stephen J. O’Brien 6,71Department of Evolution and Ecology and the UC Davis Genome Center, 4321 Genome and BiomedicalSciences Facility, University of California, Davis, CA 95616, USA; 2Department of Ecology, Environment andEvolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Bundoora , Victoria 3086, Australia;3San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA;4Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia; 5Novosibirsk State University,Novosibirsk 630090, Russia; 6Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg StateUniversity, St. Petersburg 194044, Russia and 7Halmos College of Natural Sciences and Oceanography, NovaSoutheastern University, Ft. Lauderdale, FL 33004, USA∗Correspondence address. Harris A. Lewin, UC Davis Genome Center, 4321 Genome and Biomedical Sciences Facility, University of California, Davis, CA95616, USA E-mail: lewin@ucdavis.edu http://orcid.org/0000-0002-1043-7287AbstractThe confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respectinghistorical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinctnomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (forchromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resultingcollection of C-scaffolds that represent an organism’s genome). This nomenclature avoids conflict with the historicaldefinitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of imagesof all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclaturewill assist end users to properly classify genome assemblies, thus facilitating genomic analysis.BackgroundLong-read DNA sequencing, chromatin conformation capturetechniques, and optical mapping methods now make it possibleto approach a complete, contiguous, phased, and ordered repre-sentation of the DNA sequence of chromosomes. Chromosome-level assembly is fast becoming the gold standard to be appliedto de novo whole-genome sequencing [1]. To avoid misrepresen-tation and confusion in the scientific community, there is an ur-gent need to adopt nomenclature for these assemblies that isconsistent with well-accepted definitions used in genomics andcytology.A reference-quality chromosome-scale whole-genome se-quence can now be produced de novo for a tiny fraction of theoriginal cost of sequencing the human genome. Several consor-tia are therefore actively striving to achieve near-complete andaccurately ordered genome sequences using the newly avail-able approaches. For example, the G10K-Vertebrate GenomesProject recently released new chromosome-scale assembliesof 14 vertebrate species [2] and is projecting hundreds morechromosome-scale assemblies in 2019. The Earth BioGenomeProject [3] aims to produce more than 9000 reference-quality eu-karyote genomes. Reference-quality genome sequences for largenumbers of eukaryotic taxa will greatly accelerate our under-standing of evolution, adaptation, and speciation.It has been recognized that a good physical gene mapgreatly facilitates assembly of incomplete sequences, allow-ing a correct chromosomal ordering of assembly scaffolds[4]. However, new sequencing and assembly methods nowmake it possible to build chromosome-scale scaf-Received: 25 June 2019; Revised: 16 July 2019; Accepted: 26 June 2019C© The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium,provided the original work is properly cited.1Downloaded from https://academic.oup.com/gigascience/article-abstract/8/8/giz086/5553375 by Nova Southeastern University user on 27 August 20192 Nomenclature for chromosome-scale assembliesfolds in the absence of a map or even a cytologi-cal description. This is just as well, for genome se-quencing is fast outpacing cytological studies. So far,cytological karyotypes have been complied for only 1160 ofthe 5500 named mammal species [5] and even fewer for othervertebrates and invertebrates. This means that there willsoon be species for which a fully sequenced genome, but nokaryotype, is available.Nomenclature for Assemblies of DNAFragmentsNames applied in the literature to longer assemblies ofsequenced DNA fragments include contig, scaffold, andsuperscaffold (see Text Box). The International NucleotideSequence Database Collaboration that involves major sequencearchives now designates certain scaffold-based assemblies to begiven the designation “chromosome level” and super-scaffoldsto be named simply “chromosomes,” even in the absenceof physical mapping data (e.g., pale spear-nosed bat: [6] andgreater horseshoe bat: [7]).This contributes to substantial confusion and frequent mis-understanding. Imprecise terminology for these large scaffoldspresents an issue for users of the databases, who need to quan-tify how complete a deposited genome sequence actually is,as well as to distinguish assemblies that have comprehensivephysical assignments to chromosomes from those that are onlyscaffold based.Perhaps even more important, it is now clear that the non-DNA components of chromosomes, particularly modified his-tones, exercise profound influence over chromosome confor-mation and the expression of genes in development, as wellas change as the result of environmental influences (epigeneticvariation) [8, 9]. In addition, the position of genes on the chromo-some with respect to its centromere, telomeres, and heterochro-matin, as well as the position of a chromosome in the interphasenucleus of the cell, can affect expression. Thus, studies of chro-mosome evolution, the evolution of gene regulation by changesin chromosome conformation, and epigenetics all require orbenefit from distinguishing scaffold-based versus chromosome-anchored assemblies versus functional chromosomes.Proposed NomenclatureThere are, therefore, different ways to describe elements of aspecies’ genome. Descriptors sometimes overlap but must oftenbe distinguished. We define established terms in the Text Boxand propose new specific terms for chromosome-scale assem-blies in order to:1) avoid conflict with established terminology,2) avoid problems downstream for species with a scaffold-only-based representation of its chromosomes and for which nokaryotype is available, and3) make clear to end users of the new assemblies exactly whatis being described.We justify the distinction of the new terms as follows. Theterm chromosome (from Greek roots for “colored body”) wascoined in 1888 [10]. A century ago chromosomes were found tocontain the genes of an organism. In eukaryotes, chromosomesare widely recognized as DNA-protein complexes housing a sin-gle linear DNA molecule that bears a linear array of genes. Chro-mosomes during cell interphase exist as long threadlike chro-matin in the nucleus, but during mitosis, they contract into rod-shaped bodies that can be visualized using microscopy. Thus,the term chromosome has a clear definition that has been in usefor 130 years.A DNA scaffold, no matter how large or complete, can neverbe a chromosome. It is a simply an abbreviated digital script ofthe linear DNA sequence on a chromosome. For assignment ofDNA sequence to a chromosome, it must be physically mappedby methods such fluorescence in situ hybridization or by infer-ence if a scaffold includes DNA marker sequences that were pre-viously mapped.DNA sequencing technology has not yet advanced to pro-duce a single molecule that represents an entire chromosomein any large multicellular eukaryote. However, in the future, anew generation of long-read technology may yield contiguousfragments that span the entire chromosome length, most likelyfor eukaryotes with small genomes. Ungapped contiguous over-lapping fragments of DNA sequence are termed contigs, and forconsistency with the proposed nomenclature for chromosome-scale scaffolds (see below), we propose the term chromosome-scale contig, or C-contig, to define an ungapped assembly of DNAfragments that spans an entire chromosome (autosome or sexchromosome) or the circular genome of mitochondria. Suchcontigs have been produced for bacterial chromosomes andchromosomes of yeasts and fungi (e.g., Saccharomyces cerevisiae,Kluyveromyces lactis, and Candida dubliniensis).We propose to name a scaffold or super-scaffold that appearsto span the full length of a chromosome or a chromosome armas a chromosome-scale scaffold, abbreviated as C-scaffold. Even withthe powerful technologies available today, for the vast majorityof eukaryotic species, the largest scaffolds have appreciable se-quence gaps and are frequently missing highly repetitive regionssuch as centromeres and telomeres. Thus, chromosome armswill often be the largest units that can be completely representedby a C-scaffold.In the same way, the term karyotype (derived from the Greekword karyon, meaning “nucleus”) has been used for a centuryto describe the complete chromosome complement of a cell ororganism. In modern times a karyotype is represented as anordered array (usually by descending size) of metaphase chro-mosomes in a photographic or diagrammatic image, with cen-tromere position and any abnormalities noted. An ordered arrayof C-scaffolds (and/or C-contigs) is not the same thing and needsa new name. We propose the term scaffotype.Most eukaryotic assemblies to date include more scaffoldsthan chromosomes or chromosome arms. Thus, it is impossi-ble to determine exactly from the scaffolds the actual numberof chromosomes of a species. We recommend that karyotypesof sequenced organisms be assessed when feasible, certainlyfor reference-quality genomes of representative species. In ourview, the ultimate goal for an ideal genome assembly is to pro-duce a scaffotype of C-scaffolds (or, in the future, C-contigs) thathave all been assigned to physical chromosomes; thus, the scaf-fotype becomes a complete molecular description of a species’linear nucleotide sequence, matched to its karyotype.ConclusionsPrecise and accurate terminology is a requisite hallmark of goodscience. In biology, the definition of terms is sometimes am-biguous or misappropriated. Extensive use of jargon compli-cates matters even further. We believe that it is early enoughon the journey of producing chromosome-scale de novo assem-Downloaded from https://academic.oup.com/gigascience/article-abstract/8/8/giz086/5553375 by Nova Southeastern University user on 27 August 2019Lewin et al. 3blies to implement terminology formally that accurately reflectschromosome-scale in silico constructs of DNA fragments withoutaltering existing definitions that have served the genetics com-munity so well.Box: Terms and definitions of cytogenetics and largesequence arraysStandard Cytogenetic DefinitionsChromosome (literally “colored body”): DNA and protein-containing structure in cells of eukaryotes, microscopicallyvisible as a rod-shaped body during cell division metaphase.Karyotype: A photographic or diagrammatic image of thecomplete set of metaphase chromosomes in cells of an or-ganism of a particular species.Standard Molecular DescriptorsContigs: Contiguous gapless stretches of DNA sequence as-sembled from smaller overlapping sequenced fragments.Scaffolds: Computationally ordered and oriented arrays ofcontigs that have sequence gaps along their length.Super-scaffolds: Ordered scaffolds produced by methodssuch as optical mapping and chromosome conformationcapture technologies .Proposed New TermsC-contig (chromosome-scale contig): A contig that appearsto span all of a chromosome arm or a complete chromo-some.C-scaffold (chromosome-scale scaffold): A scaffold or super-scaffold that appears to span all of a chromosome arm or acomplete chromosome.Evidence that a contig, scaffold, or super-scaffold representsa chromosome or chromosome arm can come from Hi-Cdata and be corroborated by optical maps.A C-contig or C-scaffold is formally assigned to a chromo-some when it is physically mapped to a known chromo-some in a species having an established karyotype (e.g., us-ing fluorescence in situ hybridization). For fluorescence insitu hybridization, we recommend that multiple includedDNA markers be mapped along the length of the C-scaffold,to establish orientation.Scaffotype: A set of C-scaffolds and/or C-contigs that are arepresentation of all the chromosomes, including sex chro-mosomes, of a species.The C-scaffolds and C-contigs in a scaffotype should benumbered continuously according to descending length inthe assembly.If the C-scaffolds and C-contigs are all mapped to chromo-somes, and the number of chromosomes and C-scaffoldsis identical, then the scaffotype and the karyotype termsreflect equivalent representations of the complete chromo-some complement of an organism or species.Authors’ contributionsAll authors contributed equally to the manuscript. H.A.L J.A.M.Gand S.J.O.Editor’s NoteThis is an ongoing discussion in the community and will be de-bated and discussed this month at the upcoming G10K-VGP/EBPMeeting at Rockerfeller University (27-30th August 2019). We en-courage comments and feedback to aid in forming a consensuson the most suitable nomenclature for chromosome level se-quence. One way to discuss these matters is via social mediaand annotation of this paper by hypothes.is (use the hashtag/tag#chromosomenomenclature). We hope GigaScience can be a fo-rum to assist this discourse.AcknowledgmentsWe have widely consulted, debated with, and tried to distillthe learned responses and opinions of many members of thegenomics and cytogenetics communities. We thank particu-larly the VGP assembly group, including Erich Jarvis (also forcomments on the manuscript), Joana Damas, Adam Phillippy,Kerstin Howe, Gene Myers, David Haussler, Richard Durbin,Gavin Naylor, Mark Diekens, Andrew Crawford, Edward Braun,William Murphy, Robert Hanner, Robert Kraus, Graham Ether-ington, Karen Dyer Montgomery, Guojie Zhang, Paul Flicek, andFrançoise Thibaud-Nissen. We acknowledge that the opinionsexpressed in this article are not universally shared among allindividuals listed above.References1. Editorial. A reference standard for genome biology. NatBiotechnol2018;36:1121.2. https://vgp.github.io/genomeark/. Accessesd on June 1, 2019.3. Lewin HA, Robinson GE, Kress WJ et al. Earth BioGenomeProject: Sequencing life for the future of life. Proc Natl AcadSci2018;115:4325–33.4. Lewin HA, Larkin DM, Pontius J, O’Brien SJ. Every genome se-quence needs a good map. Genome Res2009;19:1925–8.5. Graphodatsky A, Perelman P, O’Brien SJ. An Atlas of Mam-malian Chromosomes, 2nd ed. New York, NY: John Wiley &Sons, 2019.6. Pale spear-nosed bat genome assembly. https://www.ncbi.nlm.nih.gov/assembly/GCF 004126475.1. Accessed May 1620197. Greater horseshoe bat genome assembly. https://www.ncbi.nlm.nih.gov/assembly/GCA 004115265.2. Accessed on May17, 20198. Goldberg AD, Allis CD, Bernstein E. Epigenetics: a landscapetakes shape. Cell2007;128:635–8.9. Stadhouders R, Filion GJ, Graf T. Transcription factorsand 3D genome conformation in cell-fate decisions.Nature2019;569:345–54.10. von Waldeyer-Hartz HWG. Über Karyokinese und ihreBeziehungen zu den Befruchtungsvorgängen. ArchMikroskop Anat Entwicklungsmechanik1888;32:1–122.Downloaded from https://academic.oup.com/gigascience/article-abstract/8/8/giz086/5553375 by Nova Southeastern University user on 27 August 2019

Precision nomenclature for the new genomics

The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images of all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclature will assist end users to properly classify genome assemblies, thus facilitating genomic analysis

Lewin, Harris A

Graves, Jennifer A Marshall

Ryder, Oliver A

Graphodatsky, Alexander S

O'Brien, Stephen J

eScholarship - University of California

UC DavisUC Davis Previously Published WorksTitlePrecision nomenclature for the new genomicsPermalinkhttps://escholarship.org/uc/item/7ff625nzJournalGigaScience, 8(8)ISSN2047-217XAuthorsLewin, Harris AGraves, Jennifer A MarshallRyder, Oliver Aet al.Publication Date2019-08-01DOI10.1093/gigascience/giz086 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaGigaScience, 8, 2019, 1–3doi: 10.1093/gigascience/giz086CommentaryCOMMENTARYPrecision nomenclature for the new genomicsHarris A. Lewin 1,*, Jennifer A. Marshall Graves2, Oliver A. Ryder3,Alexander S. Graphodatsky4,5 and Stephen J. O’Brien 6,71Department of Evolution and Ecology and the UC Davis Genome Center, 4321 Genome and BiomedicalSciences Facility, University of California, Davis, CA 95616, USA; 2Department of Ecology, Environment andEvolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Bundoora , Victoria 3086, Australia;3San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA;4Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia; 5Novosibirsk State University,Novosibirsk 630090, Russia; 6Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg StateUniversity, St. Petersburg 194044, Russia and 7Halmos College of Natural Sciences and Oceanography, NovaSoutheastern University, Ft. Lauderdale, FL 33004, USA∗Correspondence address. Harris A. Lewin, UC Davis Genome Center, 4321 Genome and Biomedical Sciences Facility, University of California, Davis, CA95616, USA E-mail: lewin@ucdavis.edu http://orcid.org/0000-0002-1043-7287AbstractThe confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respectinghistorical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinctnomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (forchromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resultingcollection of C-scaffolds that represent an organism’s genome). This nomenclature avoids conflict with the historicaldefinitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of imagesof all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclaturewill assist end users to properly classify genome assemblies, thus facilitating genomic analysis.BackgroundLong-read DNA sequencing, chromatin conformation capturetechniques, and optical mapping methods now make it possibleto approach a complete, contiguous, phased, and ordered repre-sentation of the DNA sequence of chromosomes. Chromosome-level assembly is fast becoming the gold standard to be appliedto de novo whole-genome sequencing [1]. To avoid misrepresen-tation and confusion in the scientific community, there is an ur-gent need to adopt nomenclature for these assemblies that isconsistent with well-accepted definitions used in genomics andcytology.A reference-quality chromosome-scale whole-genome se-quence can now be produced de novo for a tiny fraction of theoriginal cost of sequencing the human genome. Several consor-tia are therefore actively striving to achieve near-complete andaccurately ordered genome sequences using the newly avail-able approaches. For example, the G10K-Vertebrate GenomesProject recently released new chromosome-scale assembliesof 14 vertebrate species [2] and is projecting hundreds morechromosome-scale assemblies in 2019. The Earth BioGenomeProject [3] aims to produce more than 9000 reference-quality eu-karyote genomes. Reference-quality genome sequences for largenumbers of eukaryotic taxa will greatly accelerate our under-standing of evolution, adaptation, and speciation.It has been recognized that a good physical gene mapgreatly facilitates assembly of incomplete sequences, allow-ing a correct chromosomal ordering of assembly scaffolds[4]. However, new sequencing and assembly methods nowmake it possible to build chromosome-scale scaf-Received: 25 June 2019; Revised: 16 July 2019; Accepted: 26 June 2019C© The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium,provided the original work is properly cited.12 Nomenclature for chromosome-scale assembliesfolds in the absence of a map or even a cytologi-cal description. This is just as well, for genome se-quencing is fast outpacing cytological studies. So far,cytological karyotypes have been complied for only 1160 ofthe 5500 named mammal species [5] and even fewer for othervertebrates and invertebrates. This means that there willsoon be species for which a fully sequenced genome, but nokaryotype, is available.Nomenclature for Assemblies of DNAFragmentsNames applied in the literature to longer assemblies ofsequenced DNA fragments include contig, scaffold, andsuperscaffold (see Text Box). The International NucleotideSequence Database Collaboration that involves major sequencearchives now designates certain scaffold-based assemblies to begiven the designation “chromosome level” and super-scaffoldsto be named simply “chromosomes,” even in the absenceof physical mapping data (e.g., pale spear-nosed bat: [6] andgreater horseshoe bat: [7]).This contributes to substantial confusion and frequent mis-understanding. Imprecise terminology for these large scaffoldspresents an issue for users of the databases, who need to quan-tify how complete a deposited genome sequence actually is,as well as to distinguish assemblies that have comprehensivephysical assignments to chromosomes from those that are onlyscaffold based.Perhaps even more important, it is now clear that the non-DNA components of chromosomes, particularly modified his-tones, exercise profound influence over chromosome confor-mation and the expression of genes in development, as wellas change as the result of environmental influences (epigeneticvariation) [8, 9]. In addition, the position of genes on the chromo-some with respect to its centromere, telomeres, and heterochro-matin, as well as the position of a chromosome in the interphasenucleus of the cell, can affect expression. Thus, studies of chro-mosome evolution, the evolution of gene regulation by changesin chromosome conformation, and epigenetics all require orbenefit from distinguishing scaffold-based versus chromosome-anchored assemblies versus functional chromosomes.Proposed NomenclatureThere are, therefore, different ways to describe elements of aspecies’ genome. Descriptors sometimes overlap but must oftenbe distinguished. We define established terms in the Text Boxand propose new specific terms for chromosome-scale assem-blies in order to:1) avoid conflict with established terminology,2) avoid problems downstream for species with a scaffold-only-based representation of its chromosomes and for which nokaryotype is available, and3) make clear to end users of the new assemblies exactly whatis being described.We justify the distinction of the new terms as follows. Theterm chromosome (from Greek roots for “colored body”) wascoined in 1888 [10]. A century ago chromosomes were found tocontain the genes of an organism. In eukaryotes, chromosomesare widely recognized as DNA-protein complexes housing a sin-gle linear DNA molecule that bears a linear array of genes. Chro-mosomes during cell interphase exist as long threadlike chro-matin in the nucleus, but during mitosis, they contract into rod-shaped bodies that can be visualized using microscopy. Thus,the term chromosome has a clear definition that has been in usefor 130 years.A DNA scaffold, no matter how large or complete, can neverbe a chromosome. It is a simply an abbreviated digital script ofthe linear DNA sequence on a chromosome. For assignment ofDNA sequence to a chromosome, it must be physically mappedby methods such fluorescence in situ hybridization or by infer-ence if a scaffold includes DNA marker sequences that were pre-viously mapped.DNA sequencing technology has not yet advanced to pro-duce a single molecule that represents an entire chromosomein any large multicellular eukaryote. However, in the future, anew generation of long-read technology may yield contiguousfragments that span the entire chromosome length, most likelyfor eukaryotes with small genomes. Ungapped contiguous over-lapping fragments of DNA sequence are termed contigs, and forconsistency with the proposed nomenclature for chromosome-scale scaffolds (see below), we propose the term chromosome-scale contig, or C-contig, to define an ungapped assembly of DNAfragments that spans an entire chromosome (autosome or sexchromosome) or the circular genome of mitochondria. Suchcontigs have been produced for bacterial chromosomes andchromosomes of yeasts and fungi (e.g., Saccharomyces cerevisiae,Kluyveromyces lactis, and Candida dubliniensis).We propose to name a scaffold or super-scaffold that appearsto span the full length of a chromosome or a chromosome armas a chromosome-scale scaffold, abbreviated as C-scaffold. Even withthe powerful technologies available today, for the vast majorityof eukaryotic species, the largest scaffolds have appreciable se-quence gaps and are frequently missing highly repetitive regionssuch as centromeres and telomeres. Thus, chromosome armswill often be the largest units that can be completely representedby a C-scaffold.In the same way, the term karyotype (derived from the Greekword karyon, meaning “nucleus”) has been used for a centuryto describe the complete chromosome complement of a cell ororganism. In modern times a karyotype is represented as anordered array (usually by descending size) of metaphase chro-mosomes in a photographic or diagrammatic image, with cen-tromere position and any abnormalities noted. An ordered arrayof C-scaffolds (and/or C-contigs) is not the same thing and needsa new name. We propose the term scaffotype.Most eukaryotic assemblies to date include more scaffoldsthan chromosomes or chromosome arms. Thus, it is impossi-ble to determine exactly from the scaffolds the actual numberof chromosomes of a species. We recommend that karyotypesof sequenced organisms be assessed when feasible, certainlyfor reference-quality genomes of representative species. In ourview, the ultimate goal for an ideal genome assembly is to pro-duce a scaffotype of C-scaffolds (or, in the future, C-contigs) thathave all been assigned to physical chromosomes; thus, the scaf-fotype becomes a complete molecular description of a species’linear nucleotide sequence, matched to its karyotype.ConclusionsPrecise and accurate terminology is a requisite hallmark of goodscience. In biology, the definition of terms is sometimes am-biguous or misappropriated. Extensive use of jargon compli-cates matters even further. We believe that it is early enoughon the journey of producing chromosome-scale de novo assem-Lewin et al. 3blies to implement terminology formally that accurately reflectschromosome-scale in silico constructs of DNA fragments withoutaltering existing definitions that have served the genetics com-munity so well.Box: Terms and definitions of cytogenetics and largesequence arraysStandard Cytogenetic DefinitionsChromosome (literally “colored body”): DNA and protein-containing structure in cells of eukaryotes, microscopicallyvisible as a rod-shaped body during cell division metaphase.Karyotype: A photographic or diagrammatic image of thecomplete set of metaphase chromosomes in cells of an or-ganism of a particular species.Standard Molecular DescriptorsContigs: Contiguous gapless stretches of DNA sequence as-sembled from smaller overlapping sequenced fragments.Scaffolds: Computationally ordered and oriented arrays ofcontigs that have sequence gaps along their length.Super-scaffolds: Ordered scaffolds produced by methodssuch as optical mapping and chromosome conformationcapture technologies .Proposed New TermsC-contig (chromosome-scale contig): A contig that appearsto span all of a chromosome arm or a complete chromo-some.C-scaffold (chromosome-scale scaffold): A scaffold or super-scaffold that appears to span all of a chromosome arm or acomplete chromosome.Evidence that a contig, scaffold, or super-scaffold representsa chromosome or chromosome arm can come from Hi-Cdata and be corroborated by optical maps.A C-contig or C-scaffold is formally assigned to a chromo-some when it is physically mapped to a known chromo-some in a species having an established karyotype (e.g., us-ing fluorescence in situ hybridization). For fluorescence insitu hybridization, we recommend that multiple includedDNA markers be mapped along the length of the C-scaffold,to establish orientation.Scaffotype: A set of C-scaffolds and/or C-contigs that are arepresentation of all the chromosomes, including sex chro-mosomes, of a species.The C-scaffolds and C-contigs in a scaffotype should benumbered continuously according to descending length inthe assembly.If the C-scaffolds and C-contigs are all mapped to chromo-somes, and the number of chromosomes and C-scaffoldsis identical, then the scaffotype and the karyotype termsreflect equivalent representations of the complete chromo-some complement of an organism or species.Authors’ contributionsAll authors contributed equally to the manuscript. H.A.L J.A.M.Gand S.J.O.Editor’s NoteThis is an ongoing discussion in the community and will be de-bated and discussed this month at the upcoming G10K-VGP/EBPMeeting at Rockerfeller University (27-30th August 2019). We en-courage comments and feedback to aid in forming a consensuson the most suitable nomenclature for chromosome level se-quence. One way to discuss these matters is via social mediaand annotation of this paper by hypothes.is (use the hashtag/tag#chromosomenomenclature). We hope GigaScience can be a fo-rum to assist this discourse.AcknowledgmentsWe have widely consulted, debated with, and tried to distillthe learned responses and opinions of many members of thegenomics and cytogenetics communities. We thank particu-larly the VGP assembly group, including Erich Jarvis (also forcomments on the manuscript), Joana Damas, Adam Phillippy,Kerstin Howe, Gene Myers, David Haussler, Richard Durbin,Gavin Naylor, Mark Diekens, Andrew Crawford, Edward Braun,William Murphy, Robert Hanner, Robert Kraus, Graham Ether-ington, Karen Dyer Montgomery, Guojie Zhang, Paul Flicek, andFrançoise Thibaud-Nissen. We acknowledge that the opinionsexpressed in this article are not universally shared among allindividuals listed above.References1. Editorial. A reference standard for genome biology. NatBiotechnol2018;36:1121.2. https://vgp.github.io/genomeark/. Accessesd on June 1, 2019.3. Lewin HA, Robinson GE, Kress WJ et al. Earth BioGenomeProject: Sequencing life for the future of life. Proc Natl AcadSci2018;115:4325–33.4. Lewin HA, Larkin DM, Pontius J, O’Brien SJ. Every genome se-quence needs a good map. Genome Res2009;19:1925–8.5. Graphodatsky A, Perelman P, O’Brien SJ. An Atlas of Mam-malian Chromosomes, 2nd ed. New York, NY: John Wiley &Sons, 2019.6. Pale spear-nosed bat genome assembly. https://www.ncbi.nlm.nih.gov/assembly/GCF 004126475.1. Accessed May 1620197. Greater horseshoe bat genome assembly. https://www.ncbi.nlm.nih.gov/assembly/GCA 004115265.2. Accessed on May17, 20198. Goldberg AD, Allis CD, Bernstein E. Epigenetics: a landscapetakes shape. Cell2007;128:635–8.9. 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Precision nomenclature for the new genomics

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