Abstract:Prime C-values for 407 taxa are provided for which no published data exist, including 390 angiosperms, two gymnosperms, ten monilophytes and five lycophytes. Non-prime reports for 107 additional taxa are also provided. The prime values represent new reports for 129 genera and five families (of 303 genera and 97 families sampled). New family C-value maxima or minima are reported for Betulaceae, Ericaceae, Ranunculaceae and Sapindaceae. These data provide the basis for phylogenetic analyses of C-value variation … Show more
“…c The genome size of A . elata was considered to be approximately 0.8 Gb in this study, based on the genome sizes of related species 51 . d,e Quality-controlled WGS reads were used in the current study.…”
Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8–4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39–52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23–35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.
“…c The genome size of A . elata was considered to be approximately 0.8 Gb in this study, based on the genome sizes of related species 51 . d,e Quality-controlled WGS reads were used in the current study.…”
Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8–4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39–52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23–35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.
“…of scaffolds14,412,98510,253,6937,084,659Annotation of 248 conserved CEGMA genes (Parra et al . 2007)185 (74%) complete 203 (82%) complete + partial, 91% annotated full length124 (50%) complete 189 (76%) complete + partial, 66% annotated full length95 (38%) complete 184 (74%) complete + partial, 52% annotated full lengthN50 contig and scaffold sizes are based on the estimated genome size listed in the table.aO’Brien et al (1996).bFuchs et al (2008).cBai et al (2012).dDetermined as the number of non-N characters in the published reference sequence.Figure C1The contiguity of the loblolly pine v1.01 assembly is compared to contemporary draft conifer assemblies. Total scaffold span is plotted against a minimum scaffold size threshold.…”
Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer “super-reads,” rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp.
“…Based on current results in Kew Plant DNA C-values database (release 6.0, December 2012) described by Bennett and Leitch (2012), 57% of C-values have been estimated by flow cytometry while 37% have been estimated using Feulgen microdensitometry. In the most recent literature, 85% of genome size estimates were made using flow cytometry versus 15% by microdensitometry (Bai et al 2012).…”
Abstract:Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.Key words: oat, flow cytometry, nucleus, polyploidy.Résumé : La taille du génome est un indicateur de la distance évolutive et constitue un paramètre pour la caractéri-sation des génomes. Ici, les auteurs rapportent des estimés précis de la taille du génome chez 99 accessions appartenant à 26 espèces du genre Avena. Les auteurs montrent que la taille moyenne du génome chez les espèces diploïdes ayant un génome C (2C = 10,26 pg) est 15 % supérieure à celui des espèces ayant un génome A (2C = 8,95 pg), et que cette différence explique vraisemblablement la progression dans la taille des génomes parmi les espèces tétraploïdes, où AB < AC < CC (en moyenne, 2C = 16,76, 18,60 et 21,78 pg, respectivement). Toutes les accessions des trois espèces hexaploïdes ayant une composition génomique ACD présentaient des tailles de génome comparables (en moyenne, 2C = 25,74 pg). La taille du génome était généralement stable au sein d'une espèce, et conforme aux connaissances actuelles en ce qui a trait aux distances évolutives entre elles. Les résultats suggèrent également que la plupart des espèces polyploïdes du genre Avena ont connu une réduction de la taille du génome par rapport aux espèces diploïdes ancestrales. Les mesures de la taille du génome pourraient fournir une source additionnelle de contrôle de qualité lors de l'identification des espèces au sein de collections de ressources génétiques, particulièrement dans les cas où des espèces diploïdes et polyploïdes présentent une morphologie semblable. [Traduit par la Rédaction] Mots-clés : avoine, cytométrie en flux, noyau, polyploïdie.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
