Nuclear Genome Size Variation Research Articles

Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness.

The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.

New Insights Into the Evolution of C4 Photosynthesis Offered by the Tarenaya Cluster of Cleomaceae.

Cleomaceae is closely related to Brassicaceae and includes C3, C3–C4, and C4 species. Thus, this family represents an interesting system for studying the evolution of the carbon concentrating mechanism. However, inadequate genetic information on Cleomaceae limits their research applications. Here, we characterized 22 Cleomaceae accessions [3 genera (Cleoserrata, Gynandropsis, and Tarenaya) and 11 species] in terms of genome size; molecular phylogeny; as well as anatomical, biochemical, and photosynthetic traits. We clustered the species into seven groups based on genome size. Interestingly, despite clear differences in genome size (2C, ranging from 0.55 to 1.3 pg) in Tarenaya spp., this variation was not consistent with phylogenetic grouping based on the internal transcribed spacer (ITS) marker, suggesting the occurrence of multiple polyploidy events within this genus. Moreover, only G. gynandra, which possesses a large nuclear genome, exhibited the C4 metabolism. Among the C3-like species, we observed intra- and interspecific variation in nuclear genome size as well as in biochemical, physiological, and anatomical traits. Furthermore, the C3-like species had increased venation density and bundle sheath cell size, compared to C4 species, which likely predisposed the former lineages to C4 photosynthesis. Accordingly, our findings demonstrate the potential of Cleomaceae, mainly members of Tarenaya, in offering novel insights into the evolution of C4 photosynthesis.

Towards a better understanding of the Chenopodium album aggregate (Amaranthaceae) in the Middle East: A karyological, cytometric and morphometric investigation

AbstractThe study of variation in nuclear genome size, especially when combined with common garden experiments, significantly contributes to disentangling interspecies relationships within taxonomically complicated plant groups. The Chenopodium album aggregate is among the morphologically most variable groups and consists of many weakly differentiated cosmopolitan entities. We analysed nuclear genome size variation in diploid and polyploid species of the aggregate from Iran using flow cytometry of 282 accessions from 88 populations of 7 species. To this end, we also determined chromosome numbers and performed a morphometric study to reveal the extent of intraspecific morphological variation. We found that Iranian species are exclusively diploid (C. vulvaria), tetraploid (C. novopokrovskyanum, C. strictum, C. sosnowskyi and C. chaldoranicum) or hexaploid (C. album subsp. album, C. album subsp. iranicum and C. opulifolium). Six homogeneous relative genome size groups were distinguished among the species studied. Our morphometric study surprisingly revealed that under similar ecological conditions Chenopodium species are morphologically stable and well distinguishable, exhibited very little morphological variation. Hence, immense variation in leaf shapes, branching and inflorescence organization seen in the field has not been repeated under greenhouse conditions. The only exception was C. album s. str. which exhibited numerous morphotypes, covering the variation of remaining species.

Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species

BackgroundLong terminal repeat (LTR) retrotransposons are highly abundant in plant genomes and require transcriptional activity for their proliferative mode of replication. These sequences exist in plant genomes as diverse sublineages within the main element superfamilies (i.e., gypsy and copia). While transcriptional activity of these elements is increasingly recognized as a regular attribute of plant transcriptomes, it is currently unknown the extent to which different sublineages of these elements are transcriptionally active both within and across species. In the current report, we utilize next generation sequencing methods to examine genomic copy number abundance of diverse LTR retrotransposon sublineages and their corresponding levels of transcriptional activity in three diploid wild sunflower species, Helianthus agrestis, H. carnosus and H. porteri.ResultsThe diploid sunflower species under investigation differ in genome size 2.75-fold, with 2C values of 22.93 for H. agrestis, 12.31 for H. carnosus and 8.33 for H. porteri. The same diverse gypsy and copia sublineages of LTR retrotransposons were identified across species, but with gypsy sequences consistently more abundant than copia and with global gypsy sequence abundance positively correlated with nuclear genome size. Transcriptional activity was detected for multiple copia and gypsy sequences, with significantly higher activity levels detected for copia versus gypsy. Interestingly, of 11 elements identified as transcriptionally active, 5 exhibited detectable expression in all three species and 3 exhibited detectable expression in two species.ConclusionsCombined analyses of LTR retrotransposon genomic abundance and transcriptional activity across three sunflower species provides novel insights into genome size evolution and transposable element dynamics in this group. Despite considerable variation in nuclear genome size among species, relatively conserved patterns of LTR retrotransposon transcriptional activity were observed, with a highly overlapping set of copia and gypsy sequences observed to be transcriptionally active across species. A higher proportion of copia versus gypsy elements were found to be transcriptionally active and these sequences also were expressed at higher levels.

How genome size variation is linked with evolution within Chenopodium sensu lato

The significance of the wide interspecific variation in nuclear genome size of angiosperms is still not fully understood. It has been repeatedly suggested, however, that genome size can impose phenotypic constraints on plant development, phenology and ecological performance. We analysed nuclear genome size variation in diploid and polyploid species of Chenopodium s. lat. within a phylogenetic framework using flow cytometry of 456 accessions from 175 populations of 49 species: 32 diploids, 12 tetraploids, 4 hexaploids, and one decaploid. To this end, we also determined chromosome numbers and did an ITS-based phylogenetic reconstruction to analyze genome size variation using the phylogenetic generalized least-squares approach (PGLS). Results of these experiments can be summarized as follows. (1) We report the first chromosome counts for five Chenopodium species. (2) Flow cytometry determined that 2C and 1Cx DNA values differed up to 7.83- and 3.60-fold, respectively, with the lowest 1Cx value for C. schraderianum (0.412pg) [excluding tetraploid (2n=4x=32)C. ambrosioides with x=8 and 1Cx DNA content 0.279pg] and the highest for C. californicum (1.484pg). (3) Our extended phylogeny confirms the existence of previously recognized basic evolutionary lineages while underscoring the need to further increase taxon sampling for a full understanding of relationships in Chenopodioideae. (4) Our analysis of genome size evolution estimated the ancestral genome size of Chenopodium s. lat. at 0.541pg/1Cx. In addition, the data revealed a correlation between 1Cx DNA content and ploidy level. Moreover, the PGLS approach indicated that the genome size variation (i) followed the random walk model, indicating no unambiguous trend towards genome size increase or decrease; (ii) was correlated with phylogeny (λ=0.987); (iii) evolved gradually (κ=2.256); and (vi) occurred rather late after speciation, which can be attributed to species-specific adaptation (δ=3.000). (5) There are indications that several ecological traits were significantly associated with 2C DNA content. While mean plant height, maximum plant height, fruit diameter and life form were positively correlated with genome size, the species’ continent of origin showed no correlation. In summary, the strong phylogenetic signal detected in genome size of Chenopodium indicates that its genome size variation is significantly associated with phylogenetic divergence. We herein suggest a pattern of species-specific adaptations in the evolution of Chenopodium genome size.

Nuclear DNA content variation of three Miscanthus species in China

In order to estimate the variation in nuclear genome size in Miscanthus, flow cytometry of nuclei stained by propidium iodide was carried out using 36 populations of three Miscanthus species: M. lutarioriparius, M. sacchariflorus and M. sinensis, which were sampled from cold northern to warm and humid southern and central China, as well as near the sea level in eastern China to mountains in western China. The DNA content of diploid was 4.37 ± 0.02 pg/2C in M. lutarioriparius, 4.37 ± 0.01 pg/2C in M. sacchariflorus, and 5.37 ± 0.03 pg/2C in M. sinensis, respectively. There was no intraspecific variation in the three Miscanthus species at the diploid level, suggesting that the genome size was stable within species and the diverse environments did not induce variation in genome size at the diploid level. However, tetraploid populations were found in M. lutarioriparius and M. sacchariflorus, and their genome sizes were 8.56 and 8.54 pg, respectively, which are lower than expected values (8.74 pg), indicating the genome downsizing after polyploidization in the genus. Our results showed that the plant height of M. lutarioriparius was the highest one among the three species and the species was more closely related to M. sacchariflorus than M. sinensis. The intra-species genomic variation and inter-species differentiation in Miscanthus species provide important genetic and genomic information for the development of Miscanthus, especially for the endemic species, M. lutarioriparius, (together with Miscanthus × giganteus) which are now emerging as a key bio-energy crop because of their high yields and strong adaptability.

Flow cytometric analysis of genome size variation in some Passiflora species.

Nuclear genome size variation was studied in eight taxa of Passiflora. Nuclear DNA content was estimated by flow cytometry of nuclei stained by propidium iodide. 2C DNA content ranged from 3.16-5.36 pg for diploids and 1.83 pg for tetraploid. Differences in nuclear genome size were observed among Passiflora species (pg): P. suberosa 1.83, P. edulis f. edulis 3.16, P. edulis f. flavicarpa (Brazil) 3.19, P. edulis f. flavicarpa (Mexico) 3.21, P. mucronata 3.40, Passiflora edmundoi 3.43, P. laurifolia 3.88, P. giberti 3.92, P. quadrangularis 5.36, the largest value being up to 192% greater than the smallest. The means of 2C DNA content were compared by the Tukey test, and the differences in genome size permitted the recognition of five taxa groups. The result was the same for the means 2C genome size (Mbp) values. The genetic parameters were studied with their respective estimators, phenotypic variance (sigma2F), genotypic variability (PhiG), and the genotypic determination index (H2). The genotypic determination index presented high magnitude estimates (greater than 99%) emphasizing the reliability of the results and demonstrating the efficiency of determining the DNA content in the species using only one leaf per plant. Passiflora species show great phenotypic variability and have different geographic distribution that might implicate in genetic diversity.

Relationship of nuclear genome size to some reproductive cell parameters in the Florideophycidae (Rhodophyta)

Microspectrophotometry with the DNA-localizing fluorochrome 4′,6 diamidino-2-phenylindole was used to estimate nuclear genome sizes in nine species representing two orders of the Florideophycidae. Estimated 2C DNA spermatial contents in these taxa are in the range of 0.22–2.85 pg. Carpospore volume estimates determined by an image processing system for 24 species and geographical isolates representing four orders of Florideophycidae indicate mean volume ranges of 3644–233,210 μm3 for individual species, i.e. about two orders of magnitude. Estimates of carpospore numbers per cystocarp made with an image processing system indicate that carpospore volumes are negatively correlated (r = 0.716) with the number of carpospores produced per cystocarp. Three related trends were identified: (1) genome size is positively correlated with carpospore volume; (2) species with larger genomes produce fewer carpospores per cystocarp; and (3) species that produce larger carpospores produce fewer carpospores per cystocarp. These findings are discussed in the context of r– and K-selection and the evolution of nuclear genome size variation in these Florideophycidae.

Characterization of indigenousMusaspecies based on Flow Cytometric Analysis of Ploidy and Nuclear DNA Content

Ploidy and nuclear genome size variation were studied in Musa species indigenous to Malaysia i.e. Musa acuminata, Musa balbisiana, and Musa violas- cens. Flow cytometry was successfully used for ploidy estimation using DAPI and for nuclear DNA content where nuclei were stained with propidium iodide. No variation was observed in ploidy level, where as a large amount of variation in the genome size was observed among different Musa species analysed. Less variabil- ity was observed at the intraspecific level within the Musa acuminata. Similar ge- nomic DNA content were observed in Musa acuminata ssp. malaccensis (Selan- gor type) and Musa acuminata ssp. siamea (Kedah type) samples. However, the highland banana Musa acuminata ssp. truncata (Cameron type) was significantly different from two forms. Larger variation was also observed between the species Musa balbisiana (547 Mbp), and Musa violascens (680 Mbp). The genome size of Musa violascens was significantly larger than the other two species although their chromosome numbers were higher (2n=22). Statistical and cluster analysis of da- ta on genome size related in a grouping agreed well with the generally accepted taxonomic classification of Musa.

Flow cytometric analysis of nuclear DNA content in Musa

Nuclear genome size variation was studied in Musa acuminata (A genome), Musa balbisiana (B genome) and a range of triploid clones differing in genomic constitution (i.e. the relative number of A and B genomes). Nuclear DNA content was estimated by flow cytometry of nuclei stained by propidium iodide. The A and B genomes of Musa differ in size, the B genome being smaller by 12% on average. No variation in genome size was found among the accessions of M. balbisiana (average genome size 537 Mbp). Small, but statistically significant, variation was found among the subspecies and clones of M. acuminata (ranging from 591 to 615 Mbp). This difference may relate to the geographical origin of the individual accessions. Larger variation in genome size (8.8%) was found among the triploid Musa accessions (ranging from 559 to 613 Mbp). This variation may be due to different genomic constitutions as well as to differences in the size of their A genomes. It is proposed that a comparative analysis of genome size in diploids and triploids may be helpful in identifying putative diploid progenitors of cultivated triploid Musa clones. Statistical analysis of data on genome size resulted in a grouping which agreed fairly well with the generally accepted taxonomic classification of Musa.

Quantitative nuclear DNA differences associated with genome evolution in Guizotia (Compositae)

The present communication deals with 2C nuclear genome size variation in a fairly small genus Guizotia. Twenty-four accessions belonging to six species, out of seven known, were analysed in order to elucidate the extent of DNA variation both at an intra—as well as interspecific level. At the intraspecific level none of the species exhibited significant differences in their genome size. Between the species, the 2C DNA amounts ranged from 3.61 pg in G. reptans to 11.37 pg in G. zavattarii; over three-fold DNA variation is evident. Apparently these interspecific DNA differences have been achieved independent of the numerical chromosomal change(s), as all the Guizotias share a common chromosome number 2n=2x=30. The cultivated oilseed crop, G. abyssinica (7.57 pg), has accommodated nearly 78% extra DNA in its chromosome complement during the evolutionary time scale of its origin and domestication from the wild progenitor G. schimperi (4.25 pg). The extent of genomic DNA difference(s) between the species has been discussed in the light of their interrelationships and diversity.