A Catalog of Natural Channelrhodopsins

This repository is an appendix to the publication [Rozenberg20](10.1016/j.cub.2020.09.056), "Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses", that is intended to keep the list of the channelrhodopsins (ChRs) presented there as a constantly updated resource that includes updates to the old records, addition of novel unpublished entries, entries from newly published experiments and corrections to the previously published sets. Most of the credit belongs to the projects that generated and assembled the data that ultimately contained the ChRs (especially, [MMETSP_Keeling14](10.1371/journal.pbio.1001889) and [1KP_initiative19](10.1038/s41586-019-1693-2)) and to the experimentalists who took the challenge of characterizing them. The catalog currently focuses mostly but not exclusively on proteins from cultured organisms. Although the format might eventually change, the current version of the catalog is composed of two xlsx spreadsheets: Channelrhodopsins_Original_List.xlsx that represents the original ChR list with additional metadata, but without changes to the sequences and additions and without changing the classification of the ChRs. This file will remain unchanged throughout releases. It contains the following fields: ID - integer index Sequence name - unique name of the sequence Is outgroup (not ChR) - flag indicating whether the sequence is not a ChR (a small number of rhodopsins inherited from [Klapoetke14](10.1038/nmeth.2836) belonged to different families) Symbol - gene symbol, short alias Species - source species/strain Taxonomic group - taxonomic affiliation of the species ChR group - clade name, if empty indicates clades unknown back then Bioproject - NCBI bioproject for the sequence Sequence source - initiative/database/publication the gene nucleotide sequence was part of Activity - activity confirmed for the exact sequence (potentially, a shorter version or in rare cases an allelic variant thereof). In the original list, selectivity (cation/anion) was indicted for all ChRs with demonstrated channel activity even if selectivity could not be or was not assessed experimentally. Reference - publication(s) where the activity was demonstrated Full-length 98%-identity clustering: Representative - representative sequence for the cluster with an identity of 98% Cluster - cluster number Identity - identity % to the reference Rhodopsin-domain 100%-identity clustering: Representative - representative sequence for the cluster with an identity of 100% after the 98%-identity clusters were aligned and trimmed to include only the rhodopsin domain Cluster - cluster number Sequence - full protein sequence for the entry (this might be the complete sequence of the gene, partial sequence of the gene that was not recovered entirely in the assembly or sequence of a specific construct used for expression) Is partial sequence - flag indicating whether the rhodopsin domain is truncated Has indels - flag indicating whether the rhodopsin domain contains indels (unspliced introns in transcripts, gene annotation artifacts) Sequence completeness comment - comments about the nature of the indels Channelrhodopsins_Updated_List.xlsx includes amended ChR sequences, manually added entries and novel expressed or otherwise published proteins. In this release all of the sequences with complete rhodopsin domains are assigned to a family (some families have only provisional names). The spreadsheet is structured differently from the first one and focuses more on the unique complete sequences by separating genes from constructs that are derived from them. The redundancy of the dataset was further reduced by combining identical sequences. Highly similar sequences are treated mostly separately. In some cases they have been downgraded to allelic or splice variants, but this is not yet consistent. There are now three sheets: full_channelrhodopsins - full ChR sequences fragmented_channelrhodopsins - ChR sequences with incomplete rhodopsin domains not_channelrhodopsins - additional proteins that have been mentioned in ChR datasets that are not from the ChR family The sheets have the following fields: ID - integer index corresponding to the record (new records have IDs >875). Sequence name - this is the chosen sequence name for the longest version of the sequence Version - sequence version. Sequences get updated and increment their versions in the following cases: the correct start codon was identified a full sequence for the gene was found in an alternative database a full sequence for the gene has been obtained or corrected from the raw data gene annotation artifacts have been corrected manually based for the genomic sequence unspliced introns were found and removed Reviewed - a somewhat arbitrary flag indicating whether the complete sequence has been manually reviewed Constructs - NCBI protein accessions of constructs overlapping with the gene indicating the overlapping region. Note that construct are allowed to overlap multiple full-length genes even from nominally different species. Symbol - short gene alias Species - species from which the longest representative sequence belongs Taxonomic group ChR group - ChR affiliation based on phylogeny ChR supergroup - ChR supergroup (A: ACRs and green algal CCRs, B: "bacteriorhodopsin-like" CCRs, D: the clade of dinoflagellate and related colpodellid ChRs) Bioproject - bioproject accession(s) for the data from which the sequence is derived Sequence source - one or multiple sources for the sequence, preference is given to earlier released publications Source type - the kind of source(s) (e.g. genome/transcriptome) the sequence comes from First mention - reference for the source where the gene was first indicated as a ChR. Notice that with highly similar sequences this is sometimes tricky. Currents - channeling activity. This differentiates between confirmed and unconfirmed selectivities: square brackets specify the likely but unconfirmed selectivity Cation selectivity - further details on selectivity of cation ChRs Currents reference Absorption maximum, nm Action maximum, nm Spectra references Spectra comment Representative sequence from [Rozenberg20] - representative highly similar sequence (this is inherited from the from the original file: full-length 98% clustering > rhodopsin domain 100% clustering) Sequence - the amino acid sequence Superseded identical sequences - identical sequences included in the same record (with species/strain indicated if different) Splice variants - putative minor splice variants from the same species/strain Allelic variants - putative minor allelic variations from the same species/strain Superseded included sequences - shorter sequences included in the record Superseded incorrect sequences - other sequences that are different due to artifacts Version comments - brief version history Other comments This is work in progress, use with care. If a formal citation is needed, please cite [Rozenberg20](10.1016/j.cub.2020.09.056), "Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses" and [Vierock22](10.1126/sciadv.add7729), "WiChR, a highly potassium selective channelrhodopsin for low-light one- and two-photon inhibition of excitable cells".本仓库是论文《Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses》（作者Rozenberg20，DOI:10.1016/j.cub.2020.09.056）的附录，旨在将原论文中收录的视紫红质通道蛋白（channelrhodopsins, ChRs）列表打造为持续更新的资源，涵盖原有记录的修正、新增未发表条目、新发表实验相关条目以及对既往发布数据集的校正。 本数据集的主要贡献归功于生成并组装了包含视紫红质通道蛋白的原始数据的相关项目（尤其是[MMETSP_Keeling14](10.1371/journal.pbio.1001889)与[1KP_initiative19](10.1038/s41586-019-1693-2)），以及对这些蛋白开展功能表征的实验研究者。 当前目录主要但非完全聚焦于培养生物来源的蛋白。尽管后续格式可能调整，当前版本的目录包含两份Excel（xlsx）电子表格： 1. Channelrhodopsins_Original_List.xlsx：保留原论文中的视紫红质通道蛋白列表，附加元数据，但未修改序列、未新增条目且未调整蛋白分类。该文件在所有发布版本中均保持不变，包含以下字段： - ID：整数索引 - Sequence name：序列的唯一名称 - Is outgroup (not ChR)：标记该序列是否为外群（非视紫红质通道蛋白），即该序列不属于ChR（少量源自[Klapoetke14](10.1038/nmeth.2836)的视紫红质属于其他家族） - Symbol：基因符号，即短别名 - Species：来源物种/菌株 - Taxonomic group：物种的分类学归属 - ChR group：进化分支名称，留空则代表当时分支信息未知 - Bioproject：该序列对应的NCBI生物项目编号 - Sequence source：该基因核苷酸序列所属的倡议项目、数据库或文献 - Activity：针对该确切序列已确认的活性（可能为截短版本，极少数情况下为其等位变异体）。原列表中，所有经证实具有通道活性的视紫红质通道蛋白均标注了离子选择性（阳离子/阴离子），即便该选择性未通过实验确定或无法确定 - Reference：证实该活性的相关文献 - Full-length 98%-identity clustering：全长98%同一性聚类 - Representative：该聚类的代表序列 - Cluster：聚类编号 - Identity：与代表序列的同一性百分比 - Rhodopsin-domain 100%-identity clustering：视紫红质结构域100%同一性聚类 - Representative：该聚类的代表序列（基于已对齐并修剪至仅保留视紫红质结构域的98%同一性聚类结果） - Cluster：聚类编号 - Sequence：条目对应的完整蛋白序列（可能为基因完整序列、组装中未完全获取的部分序列，或用于表达的特定构建体序列） - Is partial sequence：标记视紫红质结构域是否截短 - Has indels：标记视紫红质结构域是否包含插入缺失（indels），即转录本中未剪接的内含子、基因注释异常 - Sequence completeness comment：关于插入缺失性质的注释 2. Channelrhodopsins_Updated_List.xlsx：包含修正后的视紫红质通道蛋白序列、手动添加的条目以及新发表的表达蛋白或其他类型蛋白。本版本中，所有具有完整视紫红质结构域的序列均已归入相应家族（部分家族仅拥有暂定名称）。该电子表格的结构与第一份表格不同，更侧重独特的完整序列，将基因与其衍生的构建体分开。数据集的冗余度通过合并完全相同的序列进一步降低，高度相似的序列大多仍单独保留；部分序列已被归为等位变异或剪接变异，但该分类尚未统一。 该电子表格包含三个工作表： - full_channelrhodopsins：完整视紫红质通道蛋白序列 - fragmented_channelrhodopsins：视紫红质结构域不完整的ChR序列 - not_channelrhodopsins：在ChR数据集中提及但不属于ChR家族的额外蛋白 各工作表包含以下字段： - ID：整数索引（新记录的ID大于875） - Sequence name：选取的最长版本序列的名称 - Version：序列版本号。序列更新并递增版本号的场景包括：确定了正确的起始密码子、在其他数据库中找到该基因的完整序列、从原始数据中获取或校正了该基因的完整序列、基于基因组序列手动校正了基因注释异常、发现并移除了未剪接的内含子 - Reviewed：标记，用于指示完整序列是否已被手动审核（审核标准带有一定主观性） - Constructs：与该基因重叠的构建体的NCBI蛋白登录号，需注明重叠区域。注意单个构建体可与多个全长基因重叠，即便这些基因来自名义上不同的物种 - Symbol：基因短别名 - Species：最长代表序列所属的物种 - Taxonomic group：分类学群组 - ChR group：基于系统发育分析的ChR归属 - ChR supergroup：ChR超类群（A类：ACRs与绿藻CCRs；B类：“类细菌视紫红质”CCRs；D类：甲藻及相关Colpodellid ChRs进化分支） - Bioproject：该序列来源数据的生物项目登录号 - Sequence source：序列的一个或多个来源，优先选用较早发布的文献 - Source type：序列来源的类型（例如基因组/转录组） - First mention：该基因首次被标注为ChR的文献来源。需注意，对于高度相似的序列，该标注有时存在难度 - Currents：通道活性信息。该字段区分已确认和未确认的离子选择性：方括号标注的为推测但未经实验证实的选择性 - Cation selectivity：阳离子型ChR选择性的详细信息 - Currents reference：活性相关文献 - Absorption maximum, nm：吸收最大值（单位：纳米） - Action maximum, nm：动作光谱最大值（单位：纳米） - Spectra references：光谱相关文献 - Spectra comment：光谱相关注释 - Representative sequence from [Rozenberg20]：源自原文件的高度相似序列代表（继承自原文件的全长98%聚类>视紫红质结构域100%聚类流程） - Sequence：氨基酸序列 - Superseded identical sequences：纳入本记录的相同序列（若来源物种/菌株不同则注明） - Splice variants：同一物种/菌株的推定次要剪接变异体 - Allelic variants：同一物种/菌株的推定次要等位变异 - Superseded included sequences：纳入本记录的较短序列 - Superseded incorrect sequences：因注释异常而存在差异的其他序列 - Version comments：简要的版本历史 - Other comments：本数据集仍在开发中，使用时请谨慎。如需正式引用，请同时引用[Rozenberg20](10.1016/j.cub.2020.09.056)《Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses》以及[Vierock22](10.1126/sciadv.add7729)《WiChR, a highly potassium selective channelrhodopsin for low-light one- and two-photon inhibition of excitable cells》。