Growing and cultivating the forest genomics database, TreeGenes

Falk, Taylor; Herndon, Nic; Grau, Emily; Buehler, Sean; Richter, Peter; Zaman, Sumaira; Baker, Eliza M.; Ramnath, Risharde; Ficklin, Stephen P.; Staton, Margaret; Feltus, Frank Alexander; Jung, Sook; Main, Doreen; Wegrzyn, Jill L.

doi:10.1093/database/baz043

Cited by 19 publications

(17 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Translated UniGenes for all available gymnosperms were downloaded from the forest genomics database TreeGenes (https://treegenesdb.org/; Falk et al 2018;Wegrzyn et al 2019). The corresponding files from the Amborella trichopoda genome assembly were also included to provide an outgroup to the gymnosperm taxa.…”

Section: Orthogroup Assignment Of Proteinsmentioning

confidence: 99%

A Reference Genome Sequence for Giant Sequoia

Scott

Zimin

Puiu

et al. 2020

G3 Genes|Genomes|Genetics

Self Cite

100

View full text Add to dashboard Cite

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

show abstract

Section: Orthogroup Assignment Of Proteinsmentioning

confidence: 99%

A Reference Genome Sequence for Giant Sequoia

Scott

Zimin

Puiu

et al. 2020

G3 Genes|Genomes|Genetics

Self Cite

100

View full text Add to dashboard Cite

show abstract

“…The unavailability of reference genome assemblies constrains the scope of genomic studies in non-model species, as is the case for the vast majority of woody plant species ( Falk et al., 2018 ). In this context, the use of reduced representation genotyping methodologies, such as double-digested RAD sequencing (ddRADseq; Peterson et al., 2012 ), largely facilitates genomic analysis ( Hirsch et al., 2014 ), and has been already used in the phylogenetic analysis ( Hipp et al., 2020 ) and genetic mapping of oak species ( Konar et al., 2017 ).…”

Section: Introductionmentioning

confidence: 99%

ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Pinus taeda sequence data can be found on the PineRefSeq project on the TreeGenes platform (Falk et al, 2019;Wegrzyn et al, 2008) with the following identifier: 5A_I15_VO_L_1_T_29156/41278. Supplemental Figure 4.…”

Section: Accession Numbersmentioning

confidence: 99%

The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant specific motif and acts in a partially redundant manner with the tonoplast enzyme

Lupanga

Röhrich

Askani

et al. 2020

Preprint

View full text Add to dashboard Cite

AbstractVacuolar-type H+-ATPases (V-ATPases) are versatile proton pumps that control the pH of many intracellular compartments in all eukaryotic cells. The localization of the Arabidopsis V-ATPase was previously shown to be determined by the isoforms of subunit a (VHA-a). The incorporation of VHA-a1 targets the V-ATPase to the trans-Golgi network/early endosome (TGN/EE) whilst the incorporation of VHA-a2 or VHA-a3 targets the V-ATPase to the tonoplast. By employing chimeric proteins and site directed mutagenesis we identified a targeting domain (a1-TD) containing an acidic cluster in the N-terminus of VHA-a1 that serves as both an ER export signal and as a TGN retention motif. The a1-TD is conserved among seed plants and we confirmed experimentally that its presence is predictive of TGN/EE- localization. In contrast to many other non-seed plants, the liverwort Marchantia polymorpha encodes only a single VHA-a subunit (MpVHA-a) and we show here that it is predominantly localized at the tonoplast. In our attempts to determine if MpVHA-a can functionally replace the Arabidopsis VHA-a isoforms, we used CRISPR/Cas9 to generate null-alleles lacking VHA-a1 and discovered that its function is essential for male gametophyte development but can be replaced by VHA-a2 and VHA-a3 during vegetative growth.

show abstract

Growing and cultivating the forest genomics database, TreeGenes

Cited by 19 publications

References 0 publications

A Reference Genome Sequence for Giant Sequoia

A Reference Genome Sequence for Giant Sequoia

ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant specific motif and acts in a partially redundant manner with the tonoplast enzyme

Contact Info

Product

Resources

About