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Gordon, Sean

Publications and source records attributed to Gordon, Sean.

8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when genome sequences of known progenitors are unavailable. Existing subgenome identification methods cannot adequately infer the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus Brachypodium, which is a model genus for temperate cereals and biofuel grasses. We used a transcriptome-based phylogeny and newly designed subgenome detection algorithms coupled with a comparative chromosome barcoding analysis. Our phylogenomic subgenome detection pipeline was validated in Triticum allopolyploids, which have known progenitor genomes, and then used to infer the identities of three subgenomes derived from extant diploid species and four subgenomes derived from unknown diploid progenitors (ghost subgenomes) in six Brachypodium polyploids (B. mexicanum, B. boissieri, B. retusum, B. phoenicoides, B. rupestre and B. hybridum), of which five contain undescribed homeologous subgenomes. The existence of the seven Brachypodium progenitor genomes in the polyploids was confirmed by their karyotypic barcode profiles. Comparative phylogenomics of nuclear versus plastid trees allowed us to formulate hypothetical homoploid hybridizations and allo- and autopolyploidization scenarios that could have generated the six Brachypodium polyploids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum

Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.

35S rDNA evolution↗
NASA NTRS2017

Metadata Evaluation and Improvement: Evolving Analysis and Reporting

ESIP Community members create and manage a large collection of environmental datasets that span multiple decades, the entire globe, and many parts of the solar system. Metadata are critical for discovering, accessing, using and understanding these data effectively and ESIP community members have successfully created large collections of metadata describing these data. As part of the White House Big Earth Data Initiative (BEDI), ESDIS has developed a suite of tools for evaluating these metadata in native dialects with respect to recommendations from many organizations. We will describe those tools and demonstrate evolving techniques for sharing results with data providers.

metadata recommendations↗
NASA NTRS2017

Documentation Resources on the ESIP Wiki

The ESIP community includes data providers and users that communicate with one another through datasets and metadata that describe them. Improving this communication depends on consistent high-quality metadata. The ESIP Documentation Cluster and the wiki play an important central role in facilitating this communication. We will describe and demonstrate sections of the wiki that provide information about metadata concept definitions, metadata recommendation, metadata dialects, and guidance pages. We will also describe and demonstrate the ISO Explorer, a tool that the community is developing to help metadata creators.

ESIP Documentation Cluster↗
NASA NTRS2016

Evaluating and Evolving Metadata in Multiple Dialects

Despite many long-term homogenization efforts, communities continue to develop focused metadata standards along with related recommendations and (typically) XML representations (aka dialects) for sharing metadata content. Different representations easily become obstacles to sharing information because each representation generally requires a set of tools and skills that are designed, built, and maintained specifically for that representation. In contrast, community recommendations are generally described, at least initially, at a more conceptual level and are more easily shared. For example, most communities agree that dataset titles should be included in metadata records although they write the titles in different ways.

metadata quality↗
DOE OSTI2015

Using the Model Perennial Grass Brachypodium sylvaticum to Engineer Resistance to Multiple Abiotic Stresses

We are using the perennial model grass Brachypodium sylvaticum to identify combinations of transgenes that enhance tolerance to multiple, simultaneous abiotic stresses. The most successful transgene combinations will ultimately be used to create improved switchgrass (Panicum virgatum L.) cultivars. To further develop B. sylvaticum as a perennial model grass, and facilitate our planned transcriptional profiling, we are sequencing and annotating the genome. We have generated ~40x genome coverage using PacBio sequencing of the largest possible size selected libraries (18, 22, 25 kb). Our initial assembly using only long-read sequence contained 320 Mb of sequence with an N50 contig length of 315 kb and an N95 contig length of 40 kb. This assembly consists of 2,430 contigs, the largest of which was 1.6 Mb. The estimated genome size based on c-values is 340 Mb indicating that about 20 Mb of presumably repetitive DNA remains yet unassembled. Significantly, this assembly is far superior to an assembly created from paired-end short-read sequence, ~100x genome coverage. The short-read-only assembly contained only 226 Mb of sequence in 19k contigs. To aid the assembly of the scaffolds into chromosome-scale assemblies we produced an F2 mapping population and have genotyped 480 individuals using a genotype by sequence approach. One of the reasons for using B. sylvaticum as a model system is to determine if the transgenes adversely affect perenniality and winter hardiness. Toward this goal, we examined the freezing tolerance of wild type B. sylvaticum lines to determine the optimal conditions for testing the freezing tolerance of the transgenics. A survey of seven accessions noted significant natural variation in freezing tolerance. Seedling or adult Ain-1 plants, the line used for transformation, survived an 8 hour challenge down to -6 oC and 50% survived a challenge down to -9 oC. Thus, we will be able to easily determine if the transgenes compromise freezing tolerance. In the effort to develop biotechnological tools for perennial grass improvement, we have completed the transformation of B. sylvaticum with constructs containing 20 genes shown to be associated with enhanced abiotic stress tolerance in monocots. In addition, we have transformed plants with constructs containing a combination of genes (i.e. SARK::IPT- Ubi::HSR1::Ubi::NHX1) in order to simultaneously overexpress genes associated with drought + heat tolerance + salt tolerance. We generated single copy insert T1 lines for all constructs and the generation and bulking of homozygous T2 lines is well underway. In addition to our B. sylvaticum transgenics, we transformed B. distachyon with many of the same genes. Some of the transgenic B. distachyon plants subjected to a combined stress of both drought and salinity were able to produced higher yields than wild type plants. Our results indicate a great potential for the development of grasses with improved performance and yield in water-limited areas.

Gordon, Sean↗