From: Way Sung <wsung@cisunix.unh.edu>
Subject: Daphnia tRNAs
Date: Fri, 27 Jul 2007 13:19:34 -0400
Similar to the drosophila tRNA analysis, we applied two separate
tRNA identification programs, Aragorn and tRNA-SE to the daphnia
assembly.
We located 3983 tRNAs from Aragorn, and 5440 tRNAs from tRNA-SE
(there were 489 psuedo tRNAs in tRNA-SE). We combined the analyses
and determined that there was 3798 overlapping tRNAs from both
programs. These numbers are considerably greater than the number of
tRNAs from other eukaryotes [170 to 570 *]
----------------------------------------------------------------------
Daphnia tRNAs:
Predictor
Aragorn tRNA-SE Both
Total 3983 5929
Psuedo 0 489
tRNA 3983 5440 3798
-----------------------------
Codon/Anticodon table for tRNA: dpulex-tRNA_codonuse.txt
Codon use table from genes:
dpulex1_gnomon_dups.codonuse.txt = duplicated genes
dpulex1_gnomon_nodups.codonuse.txt = non-duplicated genes
-----------------------------
tRNA locations: dpulex-tRNA_analysis2.gff, dpulex-tRNA_analysis2.txt
Map view: http://wfleabase.org/release1/gbrowse/dpulex_jgi060905/
Search Landmark: tRNA:tRNA-*
-----------------------------
tRNA genes have about 50% tandem duplicates, using Anticodon
identity as duplicate. Of 3798 tRNAs, there are 1706 different
codon/scaffold genes, 473 are duplicates <= 3kb, another 400 <=
12kb, and another 1200 duplicates > 12kb / scaffold.
Reverse duplicates ("rever") are less common in nearby tRNAs than
distant ones.
Tandy count of duplicate locations per group
Group Stat Same Inside Near3k Near6k Near9k Near12k Far
all count 1706 0 473 168 121 92 1232
all freq 1.000 0.000 0.277 0.098 0.071 0.054 0.722
all rever 0 0 19 19 10 7 266
-----------------------------
* See recent review of eukaryote tRNAs, who find 170 - 570 tRNA genes
in a range of eukaryotes from yeast to man:
Diversity of tRNA genes in eukaryotes, Jeffrey M. Goodenbour and Tao Pan
Nucleic Acids Research, 2006, Vol. 34, No. 21 6137Ð6146 doi:10.1093/nar/gkl725
-----------
Notes on tRNA clusters: these are some random observations
on a few of the larger tRNA clusters seen on the genome map
scaffold_117: many Ile-Leu duplicate pairs (~50), coincide with Bacterial-infection EST
treatment, but no gene models, some Tiling expression
scaffold_122: similar to scaffold_117, Ile-Leu (+Ser) coincide with Bacterial-infect EST
Note: these Ile-Leu coincide with the *same* EST matches for bacteria: CBT01494,
not different ones at each location.
scaffold_126: Thr repeated with some Leu, Ser
scaffold_136: various ones repeated
scaffold_12: several repated clusters of 2-3 Asn-Val pairs with one Lys, some
Tiling expression
scaffold_13: Pro (only) repeated
scaffold_1456: Ala,Pro,Phe,Glu quartet repeated 4 times
scaffold_1470: Met,Arg,Lys,Ser,Gln repeated in Bacterial EST
scaffold_152: Ile-Leu repeated a bunch, some others, Tile expression
scaffold_153: Ile-Leu as scaffold_152
scaffold_161: Val-Lys pairs
scaffold_172: Glu,Phe,Pro,Ala, quartet repeated 4 times (like scaffold_1456)
scaffold_208: Ser repeated, around EST Microcytis fed
scaffold_227: Asp repeated ~ 30 times, in clusters of 4-7, coincident with EST Titan. nanopart.
scaffold_231: Gly-Trp repeated with WFes0004351, Tile expression
scaffold_238: Thr repeated , some Tile expression
scaffold_240: clusters of 5-6 repeats of Gly, Cys,
scaffold_242: Ala, Cys with various EST stresses
scaffold_246: Ile-Leu and EST Bacterial infect
scaffold_256: Gln,Leu,Arg,Pro with EST Titan. nanopart. in 5 to 6 clusters, some Tile express.
scaffold_267: Lots of Ile-Leu and EST Bacterial infect clusters
-- dgg
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