Marchantia Nomenclature

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The nomencleature rules in Marchantia polymorpha

Guidelines for gene names

  1. The wild-type allele is written in capital letters and italics.
  2. The mutant allele is written in small letters and italics. The origin of the mutant allele, whether via homologous recombination knockout, forward genetics mutagenesis, or targeted via CRISPR-CAS is irrelevant.
  3. The wild-type and mutant names, when written in full should appear in the same manner.
  4. Abbreviated gene symbols should have 2-8 letters and may be followed by a number if there are multiple loci with the same name. In the case of genes encoding microRNAs, the locus designation is a lowercase letter rather than a number.
  5. Different mutant alleles of the same gene are distinguished by a number (allele designation) following a hyphen. If only a single mutant allele is known, an allele designation is not required. Optional superscript descriptors, such as KO for homologous recombination mediated knockout, may be added.
  6. Recessive and dominant alleles are written in the same manner; if an allele is dominant to the wild-type allele, a 'd' may be added after the allele designation.
  7. Protein products should be written in capital letters, no italics.
  8. Phenotypes are designated by the gene symbol (no italics) with the first letter capitalized and followed by a superscript + or -. Thus Abc+ describes the wild type; Abc- refers to the mutant.
  9. MicroRNA nomenclature follows that outlined in Meyers et al. (Plant Cell 20:3186, 2008) and at The microRNA locus follows the standard gene nomenclature, e.g. see 1 and 2 above; the microRNA itself is written as 'MpmiRNNN'.
  10. The wild-type allele is that present in the accession whose genome was sequenced, Tak-1. If using another accession in which the allele differs substantially from that of Tak-1, it is written with the accession in superscript.
  11. Double mutants are written with alleles directly following one another.
  12. If the gene name is co-opted from a gene initially identified in another species, the name is preceded by 'Mp' (not italicized) to designate Marchantia polymorpha. In order to use the same name the M. polymorpha gene should be an ortholog, not merely a homolog. If the gene name originates in M. polymorpha, the prefix is optional.
  13. Genes in related Marchantia species will have a different prefix.

gene full nameMpALPHABETICA; with locus number
gene symbolMpABC, MpDEF2
mutant alleleMpabc
specific mutant alleleMpabc-1, Mpabc-2KO, Mpabc-3d
phenotypeMpAbc+, MpAbc-
microRNA geneMpMIR160, MpMIR166a
microRNAMpmiR160, MpmiR166
allele in another accessionMpABCKit-2
double mutantMpabc Mpdef2

Guidelines for transgene nomenclature

  1. Regulatory sequences, colloquially termed promoters, are designated with a subscript 'pro' preceding or following the name of the regulatory sequences.
  2. Transcriptional fusions are written with a single colon between the name of the regulatory sequence and the name of the coding sequence.
  3. Translational fusions are written with a '-' between the fused coding sequences, which are listed in the order they appear in the protein. This nomenclature can be extended to include the fusion of more than two coding sequences.
  4. Specific transgene alleles are written either with a hyphen and a number or a superscript designation.
  5. Artificial microRNAs are written with a amiR prefix followed by a hyphen and then the name of gene(s) that are targeted. The original backbone on which the amiR was based is designated in superscript.
  6. When using a transactivation system (e.g. GAL4/UAS or LhG4/Op) for regulating transgenes a '>>' is written between the name of the regulatory sequences and the name of the coding sequences being regulated.

promoterproMpABC or MpABCpro
transcriptional fusionproMpABC:GFP
translational fusionproMpABC:MpABC-GFP
transgene alleleproMpEF1:MpABC-1 or proMpEF1:MpABC#1
artificial miRamiR-MpABCMpmir160

Reference: Bowman et al., Plant Cell Physiol., in press. doi: 10.1093/pcp/pcv193

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