INTRODUCTION

Genome size evolution: patterns, mechanisms, andmethodological advances

It has been recognized for more than 60 years that there issubstantial variability in nuclear genome size among animals andplants, and that this diversity is unrelated to organismal complex-ity. Protein-coding gene regions typically make up a small fractionof eukaryotic genomes, and there has long been interest in thefunctions (if any) of the noncoding majority of eukaryotic DNA.The much-discussed Encyclopedia of DNA Elements (ENCODE)project, which sought to catalogue noncoding DNA sequences inthe human genome, provides a notable recent example.

In addition to in-depth analyses of individual genomes, a greatdeal of work has been done from a comparative standpoint inwhich genome sizes are compared across species. To date, genomesize estimates have been provided for more than 10 000 species ofanimals and plants (Bennett and Leitch 2012; Gregory 2013). Inplants, genome sizes vary by a factor of >2500, and in animals therange is >7000-fold. In both groups, genome size has been foundto correlate strongly with cell size, cell division rate, and a variety oforganism-level traits such as metabolic rate or developmental rate.

Over the past few years, there have been various journalissues dedicated to presenting new genome size research, forexample, Annals of Botany (Vol. 82, Suppl. 1, 1998 and Vol. 95, Iss. 1,2005), Genetica (Vol. 115, Iss. 1, 2002), Journal of Botany (2010), andPreslia (Vol. 82, Iss. 1, 2010). Most of these have focused on plants,but it is clear that there is much overlap in the topics and outcomesof research focusing on various groups of organisms. Following aproductive Genome Size workshop in 2010 hosted at the Univer-sity of Guelph and funded by the Ontario Genomics Institute, weset out to compile a collection of original papers that synthesizedsome of the exciting new research in genome size. In particular,we wanted to target the three following areas: new patterns of ge-nome size diversity across eukaryotes, mechanistic approaches tovariation in genome size, and methodological advances in estimat-ing genome size and interpreting the data. The first set of papersappeared in Chromosome Research in 2011 (Vol. 19, Issues 6 and 7), andthe second series of papers is found here, in this special issue ofGenome.

New patterns of genome size diversityThe collection of papers includes the first major surveys of ge-

nome size diversity in several previously understudied groups ofanimals and plants. Notably, Jeffrey et al. (2013) provide the firstsurvey of genome size diversity in sponges, and Smith et al. (2013)greatly increase our knowledge of variation in bat genome size.Hanrahan and Johnston (2011) contributed 134 new estimates toarthropod genome size data. In addition to expanding the bound-aries of our knowledge of DNA content variation, it is importantto look at the data we do have and prepare targets for futureresearch. In plants, we have new data for early diverging plantgroups. Bainard and Villarreal (2013) give the first comprehensivesurvey of genome size variation in hornworts, a critical group inthe land plant phylogeny suggested to be sister to extant tracheo-phytes. In addition, Pellicer et al. (2013) provide genome size andchromosome counts for the Nymphaeales, an early diverging groupof plants within the angiosperms. Bainard et al. (2011a) furthered ourunderstanding of fern and clubmoss genome size variation.

Exploring the mechanisms behind genome sizediversity

The second category of papers explores the many mechanismsthat contribute to genome size diversity. Repetitive noncodingDNA sequences, especially transposable elements, are consideredto be one of the largest contributors to genome size variation. It is,therefore, fitting that several papers in this collection explore therole of transposable elements in genome evolution (Ågren andWright 2011; Hertweck 2013; Janicki et al. 2011; Lee et al. 2013). Inaddition, Fattash et al. (2013) review the current knowledge re-garding miniature inverted repeat transposable elements (MITEs),and discuss computational advances in the discovery and analysisof MITEs. Other less often considered mechanisms of genome sizechange are considered as well. The comment by Hilliker andTaylor-Kamall (2013) gives insight into the genic function of het-erochromatin and how it may be linked to variation in genomesize. Wyngaard et al. (2011) explored the unique occurrence ofchromatin diminution in copepods. Additionally, Dufresne andJeffery (2011) provided a more general discussion of the evolutionof particularly large genomes in animals.

Methodological advances in genome size researchBoth broad comparative analyses of genome size diversity and

detailed studies focused on single species have benefited fromtechnological advances in recent years. Nevertheless, it is impor-tant that the limits of these methods be examined empirically sothat sources of error can be identified. Several papers in this col-lection deal with methodological topics that are relevant in thisregard. Gregory et al. (2013) test the use of qPCR for genome sizeestimation and the purported role of rearing conditions in affect-ing genome size estimates in Drosophila. Interestingly, while theyfind that rearing conditions do not considerably alter estimates ofDNA content, Jalal et al. (2013) find evidence for such an effect inDaphnia. This suggests that environmental conditions may differ-entially affect DNA condensation and resulting genome size esti-mates for different species. Bainard et al. (2011b) explored the useof desiccated plant tissue for flow cytometric analysis and foundthat, in many cases, the effect of drying was small enough to makethe use of this preservation method feasible in field studies.

Advances in methodological approaches apply not only to theestimation of genome size but also in our interpretation ofgenomic data. Saylor et al. (2013) approach the Bos taurus genomefrom an ecological perspective, and Kelly and Leitch (2011) explorelarge plant genomes using next-generation sequencing.

Moving forwardAs the papers provided in these recent collections demonstrate,

genome size is an active area of research. Developing a good under-standing of the factors that shape the size of a genome is of interestin a wide range of biological disciplines. The papers provide a strongindication that progress is being made in this area, and that manynew insights are sure to be discovered in the coming years.

J.D. BainardGuest EditorDepartment of Plant Sciences, University of Saskatchewan, Saska-toon SK, S7N 5A8, Canada

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Genome 56: vii–viii (2013) dx.doi.org/10.1139/gen-2013-0170 Published by NRC Research Press

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T.R. GregoryGuest EditorDepartment of Integrative Biology, University of Guelph, GuelphON, N1G 2W1, Canada

ReferencesÅgren, J.A., and Wright, S.I. 2011. Co-evolution between transposable elements

and their hosts: a major factor in genome size evolution? Chromosome Res.19(6): 777–786. doi:10.1007/s10577-011-9229-0. PMID:21850458.

Bainard, J.D., and Villarreal, J.C. 2013. Genome size increases in recently di-verged hornwort clades. Genome, 56. This issue. doi:10.1139/gen-2013-0041.

Bainard, J.D., Henry, T.A., Bainard, L.D., and Newmaster, S.G. 2011a. DNA contentvariation in monilophytes and lycophytes: large genomes that are not endo-polyploid. Chromosome Res. 19(6): 763–775. doi:10.1007/s10577-011-9228-1.PMID:21847691.

Bainard, J.D., Husband, B.C., Baldwin, S.J., Fazekas, A.J., Gregory, T.R.,Newmaster, S.G., and Kron, P. 2011b. The effects of rapid desiccation onestimates of plant genome size. Chromosome Res. 19(6): 825–842. doi:10.1007/s10577-011-9232-5. PMID:21870188.

Bennett, M.D., and Leitch, I.J. 2012. Plant DNA C-values database. Available fromhttp://data.kew.org/cvalues/.

Dufresne, F., and Jeffery, N. 2011. A guided tour of large genome size in animals:what we know and where we are heading. Chromosome Res. 19(7): 925–938.doi:10.1007/s10577-011-9248-x. PMID:22042526.

Fattash, I., Rooke, R., Wong, A., Hui, C., Luu, T., Bhardwaj, P., and Yang, G. 2013.Miniature inverted-repeat transposable elements: discovery, distribution,and activity. Genome, 56. This issue. doi:10.1139/gen-2012-0174.

Gregory, T.R. 2013. Animal genome size database. Available from http://www.genomesize.com.

Gregory, T.R., Nathwani, P., Bonnett, T.R., and Huber, D.P.W. 2013. Sizing uparthropod genomes: an evaluation of the impact of environmental variationon genome size estimates by flow cytometry and the use of qPCR as a methodof estimation. Genome, 56. This issue. doi:10.1139/gen-2013-0044.

Hanrahan, S.J., and Johnston, J.S. 2011. New genome size estimates of 134 species

of arthropods. Chromosome Res. 19(6): 809–823. doi:10.1007/s10577-011-9231-6.PMID:21877225.

Hertweck, K.L. 2013. Assembly and comparative analysis of transposable ele-ments from low coverage genomic sequence data in Asparagales. Genome,56. This issue. doi:10.1139/gen-2013-0042.

Hilliker, A.J., and Taylor-Kamall, R.W. 2013. Heterochromatin and genome sizein Drosophila. Genome, 56. This issue. doi:10.1139/gen-2013-0157.

Jalal, M., Wojewodzic, M.W., Laane, C.M.M., and Hessen, D.O. 2013. LargerDaphnia at lower temperature: a role for cell size and genome configuration?Genome, 56. This issue. doi:10.1139/gen-2013-0004.

Janicki, M., Rooke, R., and Yang, G. 2011. Bioinformatics and genomic analysis oftransposable elements in eukaryotic genomes. Chromosome Res. 19(6): 787–808. doi:10.1007/s10577-011-9230-7. PMID:21850457.

Jeffery, N.W., Jardine, C.B., and Gregory, T.R. 2013. A first exploration of genomesize diversity in sponges. Genome, 56. This issue. doi:10.1139/gen-2012-0122.

Kelly, L.J., and Leitch, I.J. 2011. Exploring giant plant genomes with next-generation sequencing technology. Chromosome Res. 19(7): 939–953. doi:10.1007/s10577-011-9246-z. PMID:21987187.

Lee, S.-I., Park, K.-C., Son, J.-H., Hwang, Y.-J., Lim, K.-B., Song, Y.-S., et al. 2013.Isolation and characterization of novel Ty1-copia-like retrotransposons fromlily. Genome, 56. This issue. doi:10.1139/gen-2013-0088.

Pellicer, J., Kelly, L.J., Magdalena, C., and Leitch, I.J. 2013. Insights into the dy-namics of genome size and chromosome evolution in the early divergingangiosperm lineage Nymphaeales (water lilies). Genome, 56. This issue. doi:10.1139/gen-2013-0039.

Saylor, B., Elliott, T.A., Linquist, S., Kremer, S.C., Gregory, T.R., and Cottenie, K.2013. A novel application of ecological analyses to assess transposable ele-ment distributions in the genome of the domestic cow, Bos taurus. Genome,56. This issue. doi:10/1139/gen-2012-0162.

Smith, J.D.L., Bickham, J.W., and Gregory, T.R. 2013. Patterns of genome sizediversity in bats (order Chiroptera). Genome, 56. This issue. doi:10/1139/gen-2013-0046.

Wyngaard, G.A., Rasch, E.M., and Connelly, B.A. 2011. Unusual augmentation ofgermline genome size in Cyclops kolensis (Crustacea, Copepoda): further evi-dence in support of a revised model of chromatin diminution. ChromosomeRes. 19(7): 911–923. doi:10.1007/s10577-011-9234-3. PMID:21953028.

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