Scripting Analyses of Genomes in Ensembl Plants

Contreras‐Moreira, Bruno; Naamati, Guy; Rosello, Marc; Allen, James; Hunt, Sarah; Muffato, Matthieu; Gall, Astrid; Flicek, Paul

doi:10.1007/978-1-0716-2067-0_2

Cited by 14 publications

(22 citation statements)

References 50 publications

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“…In this work, we identified in silico in the A. thaliana genome the proximal SNPs in promoters of protein-coding genes for the first time, which can significantly alter the TBP binding affinity, as schematically shown in Figure 1 and quantitatively characterized in Table 1 . First of all, among Arabidopsis genes annotated in the Ensembl Plants database [ 31 ] (accessed on 16 October 2023), we selected 27,628 protein-coding genes (80%) as well as 48,321 protein-coding transcripts among 54,013 transcripts according to the current state of this database ( Table 1 : 89.5% of 100%). Then, using the automatic mode of Plant_SNP_TATA_Z-tester [ 24 ] (hereinafter, see “ Supplementary Materials ” [ 25 , 26 , 27 , 28 , 29 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ], Section S1 ), we examined separately, one-by-one each of 871,707 single nucleotide substitutions (SNPs) localized within the 90 bp proximal region adjacent to the TSS of each transcript.…”

Section: Resultsmentioning

confidence: 99%

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

Bogomolov,

Zolotareva,

Filonov

et al. 2024

IJMS

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The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.

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Section: Resultsmentioning

confidence: 99%

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

Bogomolov,

Zolotareva,

Filonov

et al. 2024

IJMS

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“…To identify the sequence of the ARF gene in Korean pine, we compared the BLAST results using ClustalW2.1 [ 35 ], Pfam ( http://pfam.xfam.org/ ) [ 36 ], and NCBI CD search programs ( https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ) [ 37 ] to eliminate redundant sequences and identify members of the PkorARF family. The amino acid and CDS length information of the PkorARF genes was downloaded from the Ensembl plants ( https://plants.ensembl.org/ ) [ 38 ]. Bioinformatics analysis was conducted on the PkorARF gene using various tools.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis)

Zhang,

Wu,

Shen

et al. 2024

BMC Plant Biol

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Background The Auxin Responsive Factor (ARF) family plays a crucial role in mediating auxin signal transduction and is vital for plant growth and development. However, the function of ARF genes in Korean pine (Pinus koraiensis), a conifer species of significant economic value, remains unclear. Results This study utilized the whole genome of Korean pine to conduct bioinformatics analysis, resulting in the identification of 13 ARF genes. A phylogenetic analysis revealed that these 13 PkorARF genes can be classified into 4 subfamilies, indicating the presence of conserved structural characteristics within each subfamily. Protein interaction prediction indicated that Pkor01G00962.1 and Pkor07G00704.1 may have a significant role in regulating plant growth and development as core components of the PkorARFs family. Additionally, the analysis of RNA-seq and RT-qPCR expression patterns suggested that PkorARF genes play a crucial role in the development process of Korean pine. Conclusion Pkor01G00962.1 and Pkor07G00704.1, which are core genes of the PkorARFs family, play a potentially crucial role in regulating the fertilization and developmental process of Korean pine. This study provides a valuable reference for investigating the molecular mechanism of embryonic development in Korean pine and establishes a foundation for cultivating high-quality Korean pine.

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“…High-confidence orthogroups produced with Ensembl Compara (Herrero et al, 2016) were retrieved with script ens_syntelogs.pl (Contreras-Moreira et al, 2022) from Ensembl Plants (Yates et al, 2022). These are derived from phylogenetic trees of aligned protein sequences from most plant species in Ensembl and have extra supporting collinearity evidence.…”

Section: Methodsmentioning

confidence: 99%

Calling pangenes from plant genome alignments confirms presence-absence variation

Contreras‐Moreira

Saraf

Naamati

et al. 2023

Preprint

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Consistent gene annotation in crops is becoming harder as genomes for new cultivars are frequently published. Gene sets from recently sequenced accessions have different gene identifiers to those on the reference accession, and might be of higher quality due to technical advances. For these reasons there is a need to define pangenes, which represent all known syntenic orthologues for a gene model and can be linked back to the original sources. A pangene set effectively summarizes our current understanding of the coding potential of a crop and can be used to inform gene model annotation in new cultivars. Here we present an approach (get_pangenes) to identify and analyze pangenes that is not biased towards the reference annotation. The method involves computing Whole Genome Alignments (WGA), which are used to estimate gene model overlaps. After a benchmark on Arabidopsis, rice, wheat and barley datasets, we find that two different WGA algorithms (minimap2 and GSAlign) produce similar pangene sets. Our results show that pangenes recapitulate known phylogeny-based orthologies while adding extra core gene models in rice. More importantly, get_pangenes can also produce clusters of genome segments (gDNA) that overlap with gene models annotated in other cultivars. By lifting-over CDS sequences, gDNA clusters can help refine gene models across individuals and confirm or reject observed gene Presence-Absence Variation. Documentation and source code are available at https://github.com/Ensembl/plant-scripts/tree/master/pangenes.

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Scripting Analyses of Genomes in Ensembl Plants

Cited by 14 publications

References 50 publications

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis)

Calling pangenes from plant genome alignments confirms presence-absence variation

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