Missing Minor Allele Frequency (MAF) data

During the update to dbSNP156 in Ensembl 111 Minor Allele Frequency (MAF) data was not imported directly to the database. This means that variants do not have an associated MAF displayed in the variant summary page as well as in the variant table in the gene tab and transcript tab in the browser. This issue is also affecting the display of variation data on the sequence views when filtering based on MAF. This data is also missing from BioMart.

Drop in paralogues from 110 to 111 for 2 species

* There is a significant drop in the number of paralogs for these 2 species: Cebus imitator and Heterocephalus glaber female

* We plan to fix this in 112

Common name misspelled obscuring search function of two bivalve molluscs

Two species of mussel (Limnoperna fortunei and Dreissena polymorpha) contain a misspelled name in their species.common_name and species.display_name. This misspelling means that these species will not be discovered web search by way of their common name ‘mussel’.

Missing variation set information prevents 1000 genomes tracks displaying correctly

If selected, the 1000 genomes short variant tracks won’t display correctly as the required information for a variant to be added to that set is missing from the database.

These tracks will be disabled in Ensembl 111.

29 Rice gene trees affected by premature pipeline synchronisation

29 gene tree nodes were slipped by premature pipeline/workflow synchronisation causing 29 trees to be affected.

Approximately, 1.16% of genes and 0.1% of the trees were missed because of this issue in rice cultivars protein trees. 

The pipeline will be re-run in release 112 and this will most likely fix the issue for the affected trees. 

Missing dbSNP156 Y variants for GRCh38

The latest dbSNP variants for the Y chromosome are missing from Ensembl 111, they will be added in release 112.

Rice genomes have missing/incongruent data

During processing of protein features for plant genomes, three rice genomes presented with missing/problematic data. The databases affected are:

• • * oryza_sativa_ir64_core_58_111_1
  • ** Error: Orphaned object_xref’s
  • ** New keys for existing identity_xref
  • ** Error: Orphaned ontology_xref’s
  • ** New keys for existing xref’s
  • ** Error: Orphaned object_xref’s
  • ** New keys for existing analysis
  • * oryza_sativa_n22_core_58_111_1
  • ** Error: Missing InterPro term names and descriptions
  • ** Error: Ascensions do not match sequences protein features
  • * oryza_sativa_arc_core_58_111_1
  • ** Error: *Missing data from DNA table*
  • ** Error: Orphaned object_xref’s
  • ** New keys for existing analysis

The new keys indicate that a key has a new id when no change should have been made.

Wheat Cactus alignment cannot be viewed on Ensembl Plants 111 website

Due to a technical issue, the Wheat Cactus alignment cannot be viewed on the Ensembl Plants 111 website.

We are working to fix the issue as soon as possible.

Missing somatic variation from ClinVar

We have missing somatic variation from ClinVar in BioMart ([https://www.ensembl.org/info/data/biomart]).

VEP Missing data for Bacteria

With our fresh load of newly annotated Bacteria species, we were unable to compute the VEP related dataset for a subset of species:

* actinomyces_naeslundii_gca_002860635

* actinomyces_urogenitalis_gca_002861525

* actinotignum_timonense_gca_002860725

* aerococcus_christensenii_gca_002861505

* bifidobacterium_longum_gca_002861445

* brevibacterium_ravenspurgense_gca_002861415

* corynebacterium_amycolatum_gca_002861405

* corynebacterium_aurimucosum_gca_002861385

* corynebacterium_coyleae_gca_002861345

* corynebacterium_coyleae_gca_002861365

* corynebacterium_riegelii_gca_002861325

* corynebacterium_tuscaniense_gca_002884935

* fusobacterium_nucleatum_gca_002884895

* gardnerella_vaginalis_gca_0028611

* gardnerella_vaginalis_gca_002861145

* gardnerella_vaginalis_gca_002861885

* gardnerella_vaginalis_gca_002861905

* gardnerella_vaginalis_gca_002861925

* gardnerella_vaginalis_gca_002862005

* gardnerella_vaginalis_gca_002884775

* kocuria_rhizophila_gca_002861865

* lactobacillus_crispatus_gca_002861805

* lactobacillus_crispatus_gca_002861815

* limosilactobacillus_pontis_gca_002940945

* micrococcus_luteus_gca_002863375

* micrococcus_luteus_gca_002884675

* moraxella_osloensis_gca_002863315

* neisseria_perflava_gca_002863305

* neisseria_sicca_gca_002863285

* oligella_urethralis_gca_002884655

* prevotella_buccalis_gca_002884635

* rothia_mucilaginosa_gca_002861015

* staphylococcus_pettenkoferi_gca_002884615

* staphylococcus_sp_umb0328_gca_002940975

* streptococcus_macedonicus_gca_002860805

* streptococcus_mitis_gca_002860825

* streptococcus_mitis_gca_002860865

* streptococcus_oralis_subsp_dentisani_gca_002860885

* streptococcus_oralis_subsp_dentisani_gca_002860905

* streptococcus_parasanguinis_gca_002860845

* streptococcus_salivarius_gca_002860765

* streptococcus_salivarius_gca_002860785

* winkia_neuii_gca_002860625

Therefore those annotations won’t be available for VEP computation this release.

Location view of GRCh38 haplotypes is broken

The “Primary assembly mapping” track is broken for some alternate regions of the GRCh38.p14 assembly version as a result of underlying changes in the database that have removed mappings between the alternate regions and the corresponding reference regions.

Since this track is turned on by default in the location view, the Region panel will show an error message.

This issue seems to affect the haplotypes only. The location view for patches seem to be correctly displayed but there won’t be any data in the “Primary assembly mapping” track.

Bug in ensembl plants compara section (Homoeologues species name discrepancy)

The genes in wheat show a list of homoeologs. Instead of the species

name (wheat) in the species column the ancestral species is shown.

Please find attached the link to the webpage and a screenshot of the

issue herewith.

[https://plants.ensembl.org/Triticum_aestivum/Gene/Compara_Homoeolog?db=core;g=TraesCS3D02G273500;r=3D:379487925-379488908;t=TraesCS3D02G273500.1] . 

Problem loading very large gene trees in Ensembl Fungi

A misconfiguration of the QuickTreeBreak step of the gene-tree pipeline led to the creation of some very large Fungi protein trees, 26 of which have more than 1500 gene members (e.g. gene tree for Aspergillus nidulans gene ANIA_07510 and Multi view of the same tree).

This is particularly noticeable for the 13 largest trees, some of which may fail to load (e.g. [https://fungi.ensembl.org/Multi/GeneTree/Image?gt=EFGT01080000065285] ).

The configuration of QuickTreeBreak has been fixed, and the issue is currently expected to be resolved in Ensembl release 112.

Missing protein-tree stats of polyploid plant genomes

Due to a software bug, statistics ‘nb_genes_in_tree’ and ‘nb_genes_unassigned’ were not calculated for polyploid genomes (e.g. “Triticum aestivum (component B)”) from Ensembl release 108 until release 111, inclusive.

The effects of this could be seen on the [Plants protein-tree statistics page|https://feb2023-plants.ensembl.org/info/genome/compara/prot_tree_stats.html?page=coverage], where polyploid genomes had statistics indicating zero genes in a tree. Knock-on effects included display of gene-tree stats pie charts which were mismatched or missing entirely.

Polyploid gene-tree statistics will be restored from Ensembl 112 onwards.

Transcript->translate() do not handle alternative codon tables correctly

Bio::EnsEMBL::Transcript->translate() does not properly translate transcripts using alternate codon tables. In particular, for the microbial codon table 11, it incorrectly translates a starting GTG as a ‘V’, instead of to an ‘M’.

Example: {*}GTG{*}TTTTCCGATATT… ==> {*}V{*}FSDIDK…

Impacts

* The change is in Transcript.pm – the `translate` method – in the Perl API

* With this change the – apparently unused (for good) – Transcript parameters `complete[35]` are going to be removed

h3. Current limitations

* The `translate` method is not – and won’t be – guaranteed to work perfectly for incomplete CDS and/or codon sequences: warnings can be raised and potentially incorrect translations may occur. This is also what has been there for several years

* The existing attributes `mRNA_start_NF`, `mRNA_end_NF`, `cds_start_NF` and `cds_end_NF` play no role in `translate`

For example, see human transcript ENST00000361453, translation ENSP00000355046.

GeneOntology Annotation drop for plants

We have observed a big drop in number of Xref imported with Gene Ontology annotation set for plants:

GO Direct import with a drop by 80% or more for Interpro, Uniprot/SWISSPROT, Uniprot/SPTREMBL:

* arabidopsis_thaliana

* arabis_alpina

* eutrema_salsugineum

* ostreococcus_lucimarinus

* pisum_sativum

* prunus_avium

Project GO Xrefs import with a drop by 66% or more for RHEA – Uniprot – Interpro – GOC

* actinidia_chinensis

* aegilops_tauschii

* amborella_trichopoda

* ananas_comosus

* arabidopsis_lyrata

* arabis_alpina

* asparagus_officinalis

* brachypodium_distachyon

* brassica_napus

* brassica_oleracea

* capsicum_annuum

* chara_braunii

* chlamydomonas_reinhardtii

* chondrus_crispus

* citrus_clementina

* coffea_canephora

* corchorus_capsularis

* cucumis_melo

* cucumis_sativus

* cynara_cardunculus

* daucus_carota

* eucalyptus_grandis

* eutrema_salsugineum

* glycine_max

* gossypium_raimondii

* helianthus_annuus

* hordeum_vulgare

* hordeum_vulgare_goldenpromise

* hordeum_vulgare_tritex

* juglans_regia

* lupinus_angustifolius

* malus_domestica_golden

* manihot_esculenta

* marchantia_polymorpha

* medicago_truncatula

* nicotiana_attenuata

* nymphaea_colorata

* oryza_indica

* oryza_sativa

* ostreococcus_lucimarinus

* panicum_hallii

* panicum_hallii_fil2

* papaver_somniferum

* phaseolus_vulgaris

* physcomitrium_patens

* pisum_sativum

* populus_trichocarpa

* prunus_avium

* prunus_dulcis

* prunus_persica

* selaginella_moellendorffii

* sesamum_indicum

* setaria_italica

* setaria_viridis

* solanum_tuberosum_rh8903916

* sorghum_bicolor

* theobroma_cacao

* triticum_urartu

* vigna_angularis

* vitis_vinifera

* zea_mays

No gene trees and no homologies for a supertree

Due to the long runtime, we had to cancel processing a gene family with 54 865 members classified together by PANTHER HMM PTHR24015 (More info on the family: [http://www.pantherdb.org/panther/family.do?clsAccession=PTHR24015].)

The genes come from the following 108 species: actinidia_chinensis, aegilops_tauschii, amborella_trichopoda, ananas_comosus, arabidopsis_halleri, arabidopsis_lyrata, arabidopsis_thaliana, arabis_alpina, asparagus_officinalis, beta_vulgaris, brachypodium_distachyon, brassica_napus, brassica_oleracea, brassica_rapa_ro18, caenorhabditis_elegans, camelina_sativa, cannabis_sativa_female, capsicum_annuum, chara_braunii, chenopodium_quinoa, chlamydomonas_reinhardtii, chondrus_crispus, ciona_savignyi, citrullus_lanatus, citrus_clementina, coffea_canephora, corchorus_capsularis, corylus_avellana, corymbia_citriodora, cucumis_melo, cucumis_sativus, cyanidioschyzon_merolae, cynara_cardunculus, daucus_carota, digitaria_exilis, dioscorea_rotundata, drosophila_melanogaster, echinochloa_crusgalli, eragrostis_curvula, eragrostis_tef, eucalyptus_grandis, eutrema_salsugineum, ficus_carica, galdieria_sulphuraria, glycine_max, gossypium_raimondii, helianthus_annuus, homo_sapiens, hordeum_vulgare, ipomoea_triloba, juglans_regia, kalanchoe_fedtschenkoi, lactuca_sativa, leersia_perrieri, lupinus_angustifolius, malus_domestica_golden, manihot_esculenta, marchantia_polymorpha, medicago_truncatula, musa_acuminata, nicotiana_attenuata, nymphaea_colorata, olea_europaea, oryza_barthii, oryza_brachyantha, oryza_glaberrima, oryza_glumipatula, oryza_indica, oryza_longistaminata, oryza_meridionalis, oryza_nivara, oryza_punctata, oryza_rufipogon, oryza_sativa, ostreococcus_lucimarinus, panicum_hallii, papaver_somniferum, phaseolus_vulgaris, physcomitrium_patens, pistacia_vera, pisum_sativum, populus_trichocarpa, prunus_avium, prunus_dulcis, prunus_persica, quercus_lobata, rosa_chinensis, saccharomyces_cerevisiae, saccharum_spontaneum, secale_cereale, selaginella_moellendorffii, sesamum_indicum, setaria_italica, setaria_viridis, solanum_lycopersicum, solanum_tuberosum, sorghum_bicolor, theobroma_cacao, trifolium_pratense, triticum_aestivum, triticum_dicoccoides, triticum_turgidum, triticum_urartu, vigna_angularis, vigna_radiata, vigna_unguiculata, vitis_vinifera, zea_mays

There will be no gene trees for the 54 865 sequences involved nor any homology information.

Inaccurate gene member homology stats in non-default gene trees

In non-default gene-tree pipelines such as Murinae (in Ensembl Vertebrates) or Protostomes (in Ensembl Metazoa), homology data is removed if it would clash with the corresponding default collection (e.g. Mouse-Rat orthologies are removed from Murinae homology data, while Loa loa paralogies are removed from Protostomes homologies).

The gene-tree pipeline for non-default collections was restructured in Ensembl 106 to ensure that such clashing homology data would be removed correctly. However, in the restructured pipeline clashing homologies are removed after the calculation of gene-member homology statistics, with the result that those statistics are inaccurate. When checked in Ensembl 110 homology data for non-default gene trees, reported gene-member homology stats were found to have a Pearson correlation coefficient with corrected gene-member homology stats in the range ~95-99%.

We plan to correct the calculation of these statistics in {*}Ensembl release 115{*}.

In the meantime, gene-member homology counts for collections other than ‘default’ should be considered as approximate, whether accessed from the ‘gene_member_hom_stats’ table of a Compara database or via Compara Perl API methods such as ‘GeneMember::number_of_orthologues’ or ‘GeneMember::number_of_paralogues’.

Missing Interpro Data

We have several species that are missing uniprot data. This is easily observed by the missing TSV  file. All protein sequences should have a uniprot ID (with the exception of bacteria) within a month of submission. New updates/added organisms are the worst affected and a majority of fungi are missing these annotations.

Missing MT ‘sequence_location’ attrib

Mitochondrial DNA sequences from 12 species (list species) were mistakenly processed as nuclear DNA sequences which then affected pairwise and multiple genome alignments, and consequently syntenies for vertebrate and metazoan genomes involved.

Subset of genes omitted from protein trees in Metazoa Compara

During a cross-check of gene members used in comparative analyses such as protein trees, the gene sets of a number of genomes in Plants, Metazoa and Pan Compara were found to be incomplete in their respective Compara databases relative to the corresponding core databases. As a result, the affected genes had been inadvertently omitted from inference of protein trees and homologies.

This issue was addressed for most affected genomes in Ensembl 112 by reloading their gene sets from their respective core databases.

Gene sets of the following affected Metazoa species will be reloaded in Ensembl 113:

* Atta cephalotes (Leaf-cutter ant)

* Bombus impatiens (Common eastern bumblebee)

* Culex quinquefasciatus (Southern house mosquito, JHB)

* Glossina fuscipes (Tsetse fly, IAEA_lab_2018)

* Musca domestica (House fly, aabys)

* Nasonia vitripennis (Jewel wasp, AsymCx)

* Solenopsis invicta (Red fire ant, M01_SB)

* Stomoxys calcitrans (Stable fly, USDA)

Canonical sequence discrepancy affecting 3299 genes in Plants Compara

During routine pre-release checks of the Ensembl site, it was found that different canonical sequences had been used in Plants and Pan Compara for 3,299 of 34,310 genes (9.6%) in {_}Brachypodium distachyon{_}. Further investigation confirmed that the Plants Compara gene members were inconsistent with their corresponding core genes.

This discrepancy will be fixed by reloading the affected gene members from their core database in Ensembl 113.

Subset of genes omitted from protein trees in Plants, Metazoa and Pan Compara

During a cross-check of gene members used in comparative analyses such as protein trees, the gene sets of a number of genomes in Plants, Metazoa and Pan Compara were found to be incomplete in their respective Compara databases relative to the corresponding core databases. As a result, the affected genes have been inadvertently omitted from inference of protein trees and homologies.

Plant species _Nicotiana attenuata_ and Metazoa species _Exaiptasia diaphana_ (Sea anemone, CC7) have been particularly badly affected by this issue, with respectively 12,351 (37%) and 13,315 (59%) of their genes omitted from comparative analyses.

To address this, gene sets of most affected genomes will be reloaded from their respective core databases in Ensembl 112 as follows.

Plants species:

* Chondrus crispus

* Nicotiana attenuata

Pan Compara species:

* Amphimedon queenslandica (Demosponge)

* Anopheles gambiae (African malaria mosquito, PEST)

* Apis mellifera (Honey bee, DH4)

* Daphnia pulex (Common water flea, KAP4)

* Drosophila melanogaster (Fruit fly)

* Gigantopelta aegis (Deep sea snail, Gae_Host)

* Hydra vulgaris (Swiftwater hydra, 105)

* Lingula anatina (Lamp shell, Amm_Jpn)

* Lytechinus variegatus (Green sea urchin, NC3)

* Parasteatoda tepidariorum (Common house spider, Goettingen)

Metazoa species:

* Acanthaster planci (Crown-of-thorns starfish)

* Acropora millepora (Stony coral, JS-1)

* Amphibalanus amphitrite (Acorn barnacle, SeventyFive)

* Anopheles gambiae (African malaria mosquito, PEST)

* Apis mellifera (Honey bee, DH4)

* Aplysia californica (California sea hare, F4 #8)

* Bombyx mori (Domestic silkworm, p50T)

* Centruroides sculpturatus (Bark scorpion, CEXI.00-Female)

* Cimex lectularius (Bed bug, Harlan)

* Crassostrea virginica (Eastern oyster, RU13XGHG1-28)

* Eurytemora affinis (Calanoid copepod, Atlantic clade)

* Exaiptasia diaphana (Sea anemone, CC7)

* Gigantopelta aegis (Deep sea snail, Gae_Host)

* Homarus americanus (American lobster, GMGI-L3)

* Hyalella azteca (Amphipod, HAZT.00-mixed)

* Hydra vulgaris (Swiftwater hydra, 105)

* Hypsibius exemplaris (Water bear tardigrade, Z151)

* Limulus polyphemus (Atlantic horseshoe crab)

* Lingula anatina (Lamp shell, Amm_Jpn)

* Lytechinus variegatus (Green sea urchin, NC3)

* Mercenaria mercenaria (Hard clam (quahog), YKG-2019)

* Orbicella faveolata (Mountainous star coral, FL)

* Parasteatoda tepidariorum (Common house spider, Goettingen)

* Penaeus japonicus (Kuruma shrimp, Ginoza2017)

* Penaeus monodon (Black tiger shrimp, SGIC_2016)

* Pollicipes pollicipes (Goose neck barnacle, AB1234)

* Priapulus caudatus (Penis worm)

* Strongylocentrotus purpuratus (Purple sea urchin, Spur 01)

* Stylophora pistillata (Hood coral, CSM Monaco)

Gene sets of the remaining affected species — all of which are in Ensembl Metazoa — will be reloaded in Ensembl 113:

* Atta cephalotes (Leaf-cutter ant)

* Bombus impatiens (Common eastern bumblebee)

* Culex quinquefasciatus (Southern house mosquito, JHB)

* Glossina fuscipes (Tsetse fly, IAEA_lab_2018)

* Musca domestica (House fly, aabys)

* Nasonia vitripennis (Jewel wasp, AsymCx)

* Solenopsis invicta (Red fire ant, M01_SB)

* Stomoxys calcitrans (Stable fly, USDA)

Regulatory activity tracks for chicken are based on incorrectly annotated data

Our regulatory build for chicken is based on public data in ENA. However, one of the ENA projects we used ([https://www.ebi.ac.uk/ena/browser/view/PRJEB45945]) has been updated since the data was processed for release 111. The relevant resubmission updated metadata associated with a few samples (see below). This means that some of our regulatory feature activity is based on incorrect sample annotation. Our peaks, signal and activity annotation have been updated for the upcoming 112 release. In the meantime, the updated files can be accessed pre-release on our ftp site ([https://ftp.ensembl.org/pub/release-112/regulation/gallus_gallus/]).

The affected epigenomes (male and female) are:

* Hindlimb muscle, 15 dpf

* Cerebellum, 15 dpf

* Cerebellum, 1 day old