Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Abstract

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

“…The genome data of Utricularia gibba PLAZA_v4 were downloaded from https://bioinformatics.psb.ugent.be (Ibarra‐Laclette et al ., ). The genome data of Solanum lycopersicum SL2.50, Solanum tuberosum SolTub_3.0, Vitis vinifera IGGP_12x, Arabidopsis thaliana TAIR10, Zea mays AGPv4 and Oryza sativa IRGSP‐1.0 were downloaded from Ensembl Genomes Release 37 (http://ensemblgenomes.org/) (Kersey et al ., ).…”

Glutamate dehydrogenases in the oleaginous yeast Yarrowia lipolytica

“…Identification of GDH encoding genes in the Y. lipolytica genome revealed only two plausible candidates (Kersey et al, ; D. J. Sherman et al, ). In order to ascertain whether ylGDH1 and ylGDH2 are indeed the only GDH enzymes in Y. lipolytica , the consequences of gene disruption were examined.…”

“…This study has provided the first in‐depth investigation of GDH enzymes in the oleaginous yeast Y. lipolytica . The YALI0F17820g gene of Y. lipolytica , here referred to as ylGDH1 , was listed in the annotated genome database as a probable NADP‐GDH based upon homologies to known enzymes (Kersey et al, ; D. J. Sherman et al, ). Indeed, the deduced amino acid sequence of ylGDH1 possesses significant similarity to the NADP‐GDH enzymes of the budding yeast S. cerevisiae (Figure S1) and complete conservation of vital active site amino acid residues deduced via structural analysis of the NADP‐GDH from A. niger (Figure S3).…”

“…Y. lipolytica genes YALI0F17820g ( ylGDH1 ) and YALI0E09603g ( ylGDH2 ), predicted to lack introns and encode potential GDHs (Kersey et al, ; D. J. Sherman et al, ), were amplified by polymerase chain reaction (PCR; for specific primer sequences, see Table S3) from DNA of Y. lipolytica strain INAG34815 (Table S1). The resulting 1.4‐kb ( ylGDH1 ) and 3.0‐kb ( ylGDH2 ) PCR fragments were gel purified, blunted using a mixture of polymerase and kinase (Quick Blunting Kit, NE Biolabs, Ipswich, MA), and ligated into the dephosphorylated Sma1 site of the S. cerevisiae pBEVY‐L vector (Miller, Martinat, & Hyman, ) under the constitutive GPD/ADH1 promoter with leucine selection.…”

“…The proper insertion of the fragments was confirmed by restriction analysis. Accuracy of the coding sequences was confirmed by sequencing (Iowa Institute of Human Genetics, Iowa City, IA) and comparison with sequences in the Y. lipolytica genome database (Kersey et al, ; D. J. Sherman et al, ). These pBEVY‐L‐ylGDH1 and pBEVY‐L‐ylGDH2 plasmids, as well as the empty vector, were then transformed into a gdh ‐null S. cerevisiae strain, ASY20A (Table S1), using the Yeastmaker™ yeast transformation system 2 (Clontech‐Takara Bio, Kyoto, Japan), and Leu+ transformants were selected.…”