Chloroplast gene nomenclature

Jonathan B. Marder MARDER at agri.huji.ac.il
Thu Jul 22 04:16:06 EST 1993


Forwarded from: Rick_Hallick at tikal.biosci.arizona.edu (Rick Hallick)
Subject: Chloroplast Gene Nomenclatu
To: MARDER at AGRI.HUJI.AC.IL (Jonathan Marder), chlamy at net.bio.net (Chlamy)
Message-id: <00132.2826107090.12014 at tikal.biosci.arizona.edu>
Organization: University of Arizona
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                       Subject:                               Time:12:48 PM
  OFFICE MEMO          Chloroplast Gene Nomenclature          Date:7/21/93
Chloroplast Gene Nomenclature has come under the auspices of the Commission
on Plant Gene Nomenclature of the International Society for Plant Molecular
Biology.  The first meeting of the Commission was held in Bellagio, Italy,
from May 3-7, 1993.  I attended as a Commission Member and Chairman of the
Working Group on Chloroplast Gene Nomenclature.  The Commission has formally
endorsed the previously published recommendations for chloroplast gene
nomenclature:

"Proposals for the Naming of Chloroplast Genes", R. B. Hallick and W.
Bottomley, Plant Molecular Biology Reporter 1, 38-43, 1983.

"Proposals for the Naming of Chloroplast Genes.  II. Update to the
Nomenclature of Genes for Thylakoid Membrane Polypeptides", R. B. Hallick,
Plant Molecular Biology Reporter 7, 266-275, 1989.

Before the next update is published (currently in draft form), I would like
to alert those in the chloroplast molecular biology community of a
significant development in the naming of open reading frames (ORFs) that are
conserved between plants, and often plants, algae, and cyanobacteria, but
for which the function is unknown.  Consider the following example:

ORF31.CHLAMY     MEALVYTFLLVGTLGIIFFSIFFRDPPRM-------IK
ORF31.EUGLENA    MEALVYTFLLIGTLGVIFFAIFFRESPRIN-------K
ORF35.MARCHANTIA MEALVYTFLLVGTLGIIFFAIFFREPPKVP---SKGKK
ORF38.WHEAT      MEALVYTFLLVSTLGIIFFAIFFREPPKVPPTPTKRIK
ORF33.MAIZE      MEALVYTFLLVSTLGIIFFAIFFREPPKVP---TKK--
ORF35.RICE       MEALVYTFLLVSTLGIIFFAIFFREPPKVP---TKKVK
ORF34.TOBACCO    MEALVYTFLLVSTLGIIFFAIFFREPPKVP---TKK-N
ORF33.SPINACH    MEALVYTFLLVSTLGIIFFAIFFREPPEISTE-----K
                 **********..***.***.****..* .

The gene for this polypeptide is variously known as orf31, orf35, orf38,
orf33, and orf34.  Genes for other proteins have also been named orf31,
orf33b, etc.  Thus, this often leads to confusion and ambiguity. The
solution proposed by the Commission on Plant Gene Nomenclature is to create
preliminary, plant-wide genes names to refer to groups of ORFs with very
similar amino acid sequences.  These temporary names will eventually be
replaced by a formal name when the gene function becomes known.  The
mnemonic for the preliminary names will be "ycf".  Y is for "hypothetical",
c is for "chloroplast", and f is for "open reading frame".  With reference
to the examples above, the orf35 genes of Marchantia and rice, which are
similar to the orf33 genes of maize and spinach, which are similar to the
orf31 genes of Euglena and Chlamydomonas, which are similar to the orf38
gene of wheat will all now be designated "ycf8".

This proposal was produced in collaboration with Amos Bairoch, University of
Geneva, director of the Swiss-Prot database. All orfs in the Swiss-Prot
database have been evaluated and cross-compared to identify candidates for
"ycf" nomenclature. The initial assignments, cross referenced with
Swiss-Prot accession number, species, and alternate names that have been
used with these genes,  are as follows:

YCF DATABASE Version 1.3  30-Jun-93
Gene Swiss Prot AC Organism Other Gene Names
ycf1 P12221 Marchantia polymorpha orf1068
ycf1 P12222 Nicotiana tabacum orf1901
ycf1 P12223 Marchantia polymorpha orf464
ycf1 P31563 Oenothera bertiana orf1005
ycf1 Q00383 Epifagus virginiana orf1738
ycf2 P08973 Spinacia oleracea orf2131
ycf2 P09975 Marchantia polymorpha orf2136
ycf2 P09976 Nicotiana tabacum orf581
ycf2 P09977 Nicotiana tabacum orf1708
ycf2 P15821 Vicia faba orfx
ycf2 P30072 Epifagus virginiana orf2216
ycf2 P31568 Oenothera picensis orf721
ycf2 P31569 Oenothera villaricae orf630
ycf3 P12202 Marchantia polymorpha orf168
ycf3 P12203 Oryza sativa orf170
ycf3 P12204 Nicotiana tabacum orf168
ycf3 P27324 Zea mays orf170
ycf4 P09362 Euglena gracilis orf206
ycf4 P12205 Marchantia polymorpha orf184
ycf4 P12206 Oryza sativa orf185
ycf4 P12207 Nicotiana tabacum orf184
ycf4 P20454 Hordeum vulgare orf130
ycf4 P25412 Aegilops squarrosa orf185
ycf4 P30981 Aegilops crassa orf185
ycf4 P30982 Triticum aestivum orf185
ycf5 P12214 Marchantia polymorpha orf320
ycf5 P12215 Oryza sativa orf321
ycf5 P12216 Nicotiana tabacum orf313
ycf5 P22554 Cryptomonas phi orf301
ycf5 P31172 Pisum sativum
ycf5 P31564 Cyanidium caldarium orf306, ccl1
ycf5 P31565 Oenothera bertiana
ycf6 P12177 Marchantia polymorpha orf29
ycf6 P12178 Nicotiana tabacum orf29
ycf6 P12178 Oryza sativa orf29
ycf7 P12179 Marchantia polymorpha orf31
ycf7 P12180 Oryza sativa orf31
ycf7 P12181 Nicotiana tabacum orf31
ycf7 P19445 Zea mays orf31
ycf8 P12182 Marchantia polymorpha orf35
ycf8 P12183 Oryza sativa orf35
ycf8 P12184 Nicotiana tabacum orf34
ycf8 P20176 Euglena gracilis orf31
ycf9 P08890 Triticum aestivum orf62
ycf9 P09973 Marchantia polymorpha orf62
ycf9 P09974 Nicotiana tabacum orf62
ycf9 P12194 Oryza sativa orf62
ycf9 P17159 Cyanophora paradoxa orf65
ycf10 P12211 Marchantia polymorpha orf434, hbp
ycf10 P12212 Oryza sativa orf230, hbp
ycf10 P12213 Nicotiana tabacum orf229, hbp
ycf10 P20150 Pisum sativum orf231, hbp
ycf10 P20864 Vicia faba n/a
ycf10 P25411 Triticum aestivum orf151
ycf11 P12217 Marchantia polymorpha orf316, zfpA
ycf11 P12218 Oryza sativa
ycf11 P12219 Nicotiana tabacum orf512, zfpA
ycf11 P18823 Pisum sativum orf371, zfpA
ycf11 P28252 Angiopteris lygofifolia orf314, dedB, zfpA
ycf11 P30064 Epifagus virginiana orf483, zfpA, dedB
ycf11 P31562 Cuscuta reflexa orf497, zfpA
ycf11 Q00761 Physcomitrella patens orf315, zfpA
ycf12 P31559 Euglena gracilis orf33
ycf12 P31560 Marchantia polymorpha orf33
ycf13 P05728 Euglena gracilis orf458
ycf13 P14761 Astasia longa orf456
ycf14 P09364 Sinapis alba orf524, matK
ycf14 P12174 Marchantia polymorpha orf370, matK
ycf14 P12175 Oryza sativa orf542, matK
ycf14 P12176 Nicotiana tabacum orf509, matK
ycf14 P17158 Hordeum vulgare matK
ycf14 P24685 Pinus contorta orf515, matK
ycf14 P30071 Epifagus virginiana orf439, matK
ycf14 Q00866 Pinus thunbergii orf515, matK
ycf15 P08974 Spinacia oleracea orf63
ycf15 P12195 Nicotiana tabacum orf70
ycf15 P31566 Oenothera villaricae orf80
ycf15 P31566 Oenothera picensis orf80
ycf16 Q02856 Antithamnion sp abcX
ycf16 Q00830 Odontella sinensis abcX

I would appreciate news about sequences and sequence comparisons of
chloroplast genes that might not yet be in the sequence databases. I would
also like information about other potential candidates for chloroplast "ycf"
nomenclature. All inquiries about chloroplast gene nomenclature can be sent
by email to:

                      hallick at arizona.edu



__
Jonathan B. Marder                 '
Department of Agricultural Botany  |     Internet: MARDER at AGRI.HUJI.AC.IL
The Hebrew University of Jerusalem | /\/ Bitnet:   MARDER at HUJIAGRI
Faculty of Agriculture             |/  \ Phone:    (08 or +9728) 481918
P.O.Box 12, Rehovot 76100, ISRAEL  /     Fax:      (08 or +9728) 467763



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