A guide to naming sequenced plant genes

Price, Colin; Reardon, Ellen M.; Lonsdale, David

doi:10.1007/bf00020109

Cited by 27 publications

(10 citation statements)

References 5 publications

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“…In the region of the K-domain, hydrophobic amino acids (L, I, V, and M) are shown in bold, and positions in which more than 75% of the sequences have a hydrophobic residue are marked by a star. The complete names of the fern genes are CRM1;Ce.ric, CRM3;Ce.ric, CRM2;Ce.pte, CRM4;Ce.pte, CRM5;Ce.pte, CRM6;Ce.pte, and CRM7;Ce.pte, which indicate their origin from different Ceratopteris species (richardii and pteroides, respectively) in accordance with recent guidelines to naming sequenced plant genes (14).…”

supporting

confidence: 69%

Floral homeotic genes were recruited from homologous MADS-box genes preexisting in the common ancestor of ferns and seed plants

Münster¹,

Pahnke²,

Rosa³

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

230

160

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Flowers sensu lato are short, specialized axes bearing closely aggregated sporophylls. They are typical for seed plants (spermatophytes) and are prominent in f lowering plants sensu stricto (angiosperms), where they often comprise an attractive perianth. There is evidence that spermatophytes evolved from gymnosperm-like plants with a fern-like mode of reproduction called progymnosperms. It seems plausible, therefore, that the stamens͞carpels and pollen sacs͞nucelli of spermatophytes are homologous to fern sporophylls and sporangia, respectively. However, the exact mode and molecular basis of early seed and f lower evolution is not yet known. Comparing f lower developmental control genes to their homologs from lower plants that do not f lower may help to clarify the issue. We have isolated and characterized MADS-box genes expressed in gametophytes and sporophytes of the fern Ceratopteris. The data indicate that at least two different MADS-box genes homologous to f loral homeotic genes existed in the last common ancestor of contemporary vascular plants, some descendants of which underwent multiple duplications and diversifications and were recruited into novel developmental networks during the evolution of f loral organs.

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supporting

confidence: 69%

Floral homeotic genes were recruited from homologous MADS-box genes preexisting in the common ancestor of ferns and seed plants

Münster¹,

Pahnke²,

Rosa³

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

230

160

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“…If there is redundancy, overlap, or confusion caused by use of the same name for different genes or different names for the same gene, the first published gene name will generally be retained and the CSGNL will work with the authors of publications to identify a new gene name and gene symbol for the subsequently reported gene(s) or loci. Genes identified in the plastid genome will be assigned names and symbols as described by the Uniprot [24], and genes identified in the mitochondrial genome will be assigned names and symbols as recommended by [21].…”

Section: No Full Namesmentioning

confidence: 99%

Gene Nomenclature System for Rice

McCouch

Linkage²

2008

Rice

345

178

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The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative has revised the gene nomenclature system for rice (Oryza) to take advantage of the completion of the rice genome sequence and the emergence of new methods for detecting, characterizing, and describing genes in the biological community. This paper outlines a set of standard procedures for describing genes based on DNA, RNA, and protein sequence information that have been annotated and mapped on the sequenced genome assemblies, as well as those determined by biochemical characterization and/or phenotype characterization by way of forward genetics. With these revisions, we enhance the potential for structural, functional, and evolutionary comparisons across organisms and seek to harmonize the rice gene nomenclature system with that of other model organisms. Newly identified rice genes can now be registered on-line at http://shigen.lab.nig. ac.jp/rice/oryzabase_submission/gene_nomenclature/.

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“…Based on their optimum temperatures for enzymatic activity, molecular sizes and epitope structures, the a-amylase isoforms were classified into two major classes and further into six subgroups. The exact corresponding relationship between genes and isoform proteins of rice a-amylase has also been determined by the Edman sequencing and peptide mass fingerprinting: a-amylase I-1 isoform is encoded by RAmy1A (ORYsa;Amy1;1, the gene names recommended by Commission on Plant Gene Nomenclature [35]), a-amylase II-3 by RAmy3E (ORYsa;Amy1;4) a-amylase II-4 by RAmy3D (ORYsa;Amy1;3) a-amylase II-5 by RAmy3B (ORYsa; Amy1; 6), and a-amylase II-6 by RAmy3C (ORYsa;Amy1;7) [28,32].…”

Section: Introductionmentioning

confidence: 99%