Three plant species have inconsistent display names
Affects: Ensembl 116	Fix versions: won’t fix
Description: Three plants are listed with inconsistent display names. Glycine soja (GCA_004193775.2) has display name: Glycine soja (Wild soybean); while the expected name should be: Glycine soja W05 Lablab purpureus (GCA_030347555.1) has display name: Lablab purpureus Natoba; while the expected name should be: Lablab purpureus Highworth Pisum sativum (GCA_024323335.2) has the display name: Pisum sativum Garden pea; while the expected name should be: Pisum sativum Zhongwan6
Workaround: No current workaround

Higher rate of dubious duplication nodes affecting Oat homologies in default Plants protein trees
Affects: Ensembl 116	Fix versions: won’t fix
Description: Due to a misconfigured species tree, a greater proportion of orthologies between Oat cultivars Sang and OT3098 have dubious duplicated ancestral nodes in the default Plants protein trees. In consequence, some orthologies between these two oat genomes may be incorrectly annotated as non tree-compliant.
Workaround: There is no workaround. Will not be fixed in 116.

Internal stop symbols in protein sequences of three vertebrate genomes
Affects: Ensembl 116	Fix versions: won’t fix
During preparation of gene member data for Vertebrates comparative processing, protein-coding member sequences were patched so that each would be consistent with its corresponding translation in the core database. This inadvertently reintroduced some protein sequences containing internal stop symbols (‘*’), which had previously been masked with ‘X’ amino-acid ambiguity codes. There are 1201 affected protein-coding genes across 3 vertebrate genomes: 602 in Mus pahari, 594 in Mus caroli and 5 in Zebrafish. The inclusion of these protein sequences with internal stop symbols may have have affected aspects of protein-tree analyses such as alignment or phylogenetic placement. The effects of this are expected to be modest in most cases. However, a minority of genes may be particularly affected. For example, in release 115 Mus caroli gene MGP_CAROLIEiJ_G0019362 was placed in the gene tree among other genes of the same species, while in release 116 this gene is placed among non-mammalian species. Users are advised to interpret with caution the protein trees and homologies of coding genes whose canonical sequence contains an internal stop symbol.
Workaround: Ensembl Vertebrates release 115 includes comparative analyses in which stop symbols have been masked with ‘X’ amino-acid ambiguity codes. Users may wish to access these via the Ensembl 115 archive site.

Cactus guide tree branch length overestimation
Affects: Ensembl 110, 111, 112, 113, 114, 115, 116 Ensembl Genomes	Fix version: won’t fix
We have discovered that the branch lengths of the guide trees used for several cactus-whole genome alignments were substantially overestimated. This was due to a bug in the component of our BUSCO-based species tree pipeline which estimates the branch lengths based on fourfold degenerate sites. The bug did not affect the topology of the guide tree, and it has effectively been fixed in the latest version of the BUSCO-based species-tree pipeline by changing the software used to produce back-translated codon alignments. This issue is unlikely to have affected the quality of the whole-genome alignments; however, the branch lengths of the guide trees stored in the HAL files of the affected alignments should not be used for downstream analyses, such as inference of conservation scores and constrained elements. The issue should not affect the inference of constrained elements using PhyloP as implemented in the HAL package, as the protocol includes the re-estimation of neutral rates. The issue likely affected the branch lengths stored in the following HAL files: https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Actinopterygii_123-way_20221206.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Aqua-faang_38-way_20220303.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Coleoptera_36-way_20230217.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Crustacea_16-way-20230217.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Lepidoptera_218-way_20230215.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Percomorpha_38-way_202203.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Pigs_27-way_20230220.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Rice_27-way_202208.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Rodent_7-way_20221018.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Wheat_37-way_20221206.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Aves-59-way_20230814.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Drosophila-40-way_20230928.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Fowl-10-way_20240131.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Mammals-100-way_20230606.hal
Workaround: The branch lengths of the guide tree must be re-estimated before downstream analyses, for example, by using the halPhyloPTrain.py script from the HAL package.

Pythium iwayamai duplicated gene models
Affects: Ensembl 116	Fix versions: won’t fix
Pythium iwayamai (DAOM BR242034) contains duplicated gene models, where different gene stable IDs correspond to identical genomic locations and structures (~380 cases identified). These duplicates may be incorrectly represented as paralogues in comparative analyses. This genome may also be referred to as Globisporangium iwayamae (DAOM BR242034) in some parts of the Ensembl Protists 116 website. A list of affected gene stable ID pairs is available below.
Workaround: No workaround. A fix will be considered for future releases on the new Ensembl site