Chloroplast Gene Nomenclatu

Rick Hallick Rick_Hallick at TIKAL.BIOSCI.ARIZONA.EDU
Wed Jul 21 15:39:53 EST 1993


                       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







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