Stofn gæsamatar (Arabidopsis thaliana) frá Íslandi greindur með aðferðum frumuerfðafræði og raðgreiningu erfðamengis

In this paper, we report the first discovery of Arabidopsis thaliana in Iceland. In May 2015, the plants were located growing on warm geothermal soil around the hot spring Deildartunguhver in Reykholt, West Iceland. Flower buds and leaves were collected and used for subsequent cytogenetic analyses and DNA sequencing. Whole plant specimens were deposited at the Icelandic AMNH herbarium and were assigned accession number VA21379. The accession was found to be diploid with 2n=2x=10, as expected for this species. At meiosis I (diakinesis) it formed five normal bivalents. Ribosomal FISH mapping revealed two pairs of 5S rDNA loci and two pairs of NORs. Fine-scale chromosome painting using BAC clones specific for chromosomes At1 and At4 confirmed the standard structure of these chromosomes. Furthermore, the painting revealed an absence of the 1.17-Mb paracentric inversion on the At4 short arm in the Icelandic accession, in contrast to the inversionbearing A. thaliana accessions more prevalent in North America. The sequencing of multiplexed whole-genome libraries identified the Swedish accession Ham-1 as the closest relative of the Icelandic accession, with, however, a markedly low SNPmatch score. We conclude that although the Icelandic accession appears to be more genetically related to populations from Scandinavia than to other European accessions, it did not originate from any of the populations represented in the global collection of the 1001 Genomes accessions of A. thaliana.Hér verður greint frá fyrsta fundi gæsamatar (Arabidopsis thaliana) á Íslandi. Tegundin fannst í maí 2015 á jarðhitasvæði við Deildartunguhver. Blómknöppum og laufblöðum var safnað fyrir litningagreiningu og raðgreiningu erfðamengis. Einnig var eintökum safnað til þurrkunar og þeim síðan komið fyrir í plöntusafni AMNH þar sem þau fengu númerið VA21379. Eins og fyrri rannsóknir gæsamatar hafa leitt í ljós reyndust sýnin vera tvílitna (2n=2x=10) og við greiningu á rýriskiptingu komu í ljós fimm eðlileg tvígilda litningapör. Þáttatenging flúrljómandi rDNA (FISH) þreifara á litningum í mítósu leiddi í ljós tvö 5S ríbósóm genapör og tvö pör NOR svæða sem jafnframt eru dæmigerð fyrir arfgerð tegundarinnar. Nánari greining með notkun BACFISH þreifara á litningunum At1 og At4 sýndi að uppbygging litninganna úr sýnunum frá Deildartungu væri eðlileg. Greiningin leiddi jafnframt í ljós vöntun á 1.17-Mb þráðhefta umhverfu á At4 litningi en þessi umhverfa er algeng meðal stofna gæsamatar í Norður-Ameríku. Raðgreining erfðamengis íslensku sýnanna leiddi í ljós mestan skyldleika við sýni frá Svíþjóð en þó með lágum skyldleikastuðli. Því er niðurstaða þessarar greiningar sú að þótt plöntur sem fundust á Íslandi séu skyldari stofnum frá Skandinavíu en stofnum annars staðar frá, hafa þær upphaflega ekki borist frá neinum af stofnum í þekktu safni 1001 erfðamengja gæsamatar víðsvegar að úr heiminum.This work was supported by EEA collaborative grant number EHP-CZ07-MOP-1-1052014.Peer Reviewe

Genomic Evidence That Governmentally Produced Cannabis sativa Poorly Represents Genetic Variation Available in State Markets

The National Institute on Drug Abuse (NIDA) is the sole producer of Cannabis for research purposes in the United States, including medical investigation. Previous research established that cannabinoid profiles in the NIDA varieties lacked diversity and potency relative to the Cannabis produced commercially. Additionally, microsatellite marker analyses have established that the NIDA varieties are genetically divergent form varieties produced in the private legal market. Here, we analyzed the genomes of multiple Cannabis varieties from diverse lineages including two produced by NIDA, and we provide further support that NIDA&rsquo;s varieties differ from widely available medical, recreational, or industrial Cannabis. Furthermore, our results suggest that NIDA&rsquo;s varieties lack diversity in the single-copy portion of the genome, the maternally inherited genomes, the cannabinoid genes, and in the repetitive content of the genome. Therefore, results based on NIDA&rsquo;s varieties are not generalizable regarding the effects of Cannabis after consumption. For medical research to be relevant, material that is more widely used would have to be studied. Clearly, having research to date dominated by a single, non-representative source of Cannabis has hindered scientific investigation. &nbsp;</p

Diversity and evolution of the repetitive genomic content in Cannabis sativa

Abstract Background The repetitive content of the genome, once considered to be “junk DNA”, is in fact an essential component of genomic architecture and evolution. In this study, we used the genomes of three varieties of Cannabis sativa, three varieties of Humulus lupulus and one genotype of Morus notabilis to explore their repetitive content using a graph-based clustering method, designed to explore and compare repeat content in genomes that have not been fully assembled. Results The repetitive content in the C. sativa genome is mainly composed of the retrotransposons LTR/Copia and LTR/Gypsy (14% and 14.8%, respectively), ribosomal DNA (2%), and low-complexity sequences (29%). We observed a recent copy number expansion in some transposable element families. Simple repeats and low complexity regions of the genome show higher intra and inter species variation. Conclusions As with other sequenced genomes, the repetitive content of C. sativa’s genome exhibits a wide range of evolutionary patterns. Some repeat types have patterns of diversity consistent with expansions followed by losses in copy number, while others may have expanded more slowly and reached a steady state. Still, other repetitive sequences, particularly ribosomal DNA (rDNA), show signs of concerted evolution playing a major role in homogenizing sequence variation

SNP dataset for M. truncatula HapMap collection

SNP database files generated using SNPmatch for Medicago truncatula HapMap collection

SNP dataset for A. thaliana RegMap panel

Biallelic SNP database files used in SNPmatch for RegMap panel of Arabidopsis thalian

SNP dataset for A. thaliana 1001 Genomes project

SNP database files generated using SNPmatch from published 1001 genomes SNP

On the causes of gene-body methylation variation in Arabidopsis thaliana.

Gene-body methylation (gbM) refers to sparse CG methylation of coding regions, which is especially prominent in evolutionarily conserved house-keeping genes. It is found in both plants and animals, but is directly and stably (epigenetically) inherited over multiple generations in the former. Studies in Arabidopsis thaliana have demonstrated that plants originating from different parts of the world exhibit genome-wide differences in gbM, which could reflect direct selection on gbM, but which could also reflect an epigenetic memory of ancestral genetic and/or environmental factors. Here we look for evidence of such factors in F2 plants resulting from a cross between a southern Swedish line with low gbM and a northern Swedish line with high gbM, grown at two different temperatures. Using bisulfite-sequencing data with nucleotide-level resolution on hundreds of individuals, we confirm that CG sites are either methylated (nearly 100% methylation across sampled cells) or unmethylated (approximately 0% methylation across sampled cells), and show that the higher level of gbM in the northern line is due to more sites being methylated. Furthermore, methylation variants almost always show Mendelian segregation, consistent with their being directly and stably inherited through meiosis. To explore how the differences between the parental lines could have arisen, we focused on somatic deviations from the inherited state, distinguishing between gains (relative to the inherited 0% methylation) and losses (relative to the inherited 100% methylation) at each site in the F2 generation. We demonstrate that deviations predominantly affect sites that differ between the parental lines, consistent with these sites being more mutable. Gains and losses behave very differently in terms of the genomic distribution, and are influenced by the local chromatin state. We find clear evidence for different trans-acting genetic polymorphism affecting gains and losses, with those affecting gains showing strong environmental interactions (G×E). Direct effects of the environment were minimal. In conclusion, we show that genetic and environmental factors can change gbM at a cellular level, and hypothesize that these factors can also lead to transgenerational differences between individuals via the inclusion of such changes in the zygote. If true, this could explain genographic pattern of gbM with selection, and would cast doubt on estimates of epimutation rates from inbred lines in constant environments

Additional file 1 of Diversity and evolution of the repetitive genomic content in Cannabis sativa

Table S1. Raw data information and repeat content for different varieties of Cannabis sativa, Humulus lupulus, Morus notabilis and Arabidopsis thaliana. Table S2. Repetitive content (percentage of the genome) in the genomes of C. sativa PK, Finola (FIN), USO31 (USO), H. lupulus (HUM) and, M. notabilis (MOR). Table S3. Repeat sequence conservation, as measured by percent sequence similarity among consensus sequences from each repeat class in each genotype, compared to the consensus repeats from the C. sativa PK genome. The missing entries are due to the absence of specific families in either of the genomes’ repeat libraries. (PDF 163 kb