Supplementary Matrials

Transcription

1 Supplementary Matrials Table S1. List of snrn genes in all analyzed insect genomes (MS Excell file) Table S2. The Honeybee genes containing 12-dependent introns. Figure S1. Models od secondary structure of the honeybee snrns. Figure S2. Phylogenetic trees of insect snrn genes.

2 ene ID Table S2. The honeybee genes containing 12-dependent introns. Representative Transcript ID 12 Intron Position* 5' Termini 3' Termini ene Family ID onsensus annotation of member proteins ENSPM ENSPMT (2) T ENSF ctin related 2/3 complex subunit 5 ENSPM ENSPMT (7) T ENSF ctivator 1.40 kda subunit replication factor c 40 kda ENSPM ENSPMT (2) T ENSF dp ribosylation factor ENSPM ENSPMT (1) T ENSF dult male small intestine cdna product:metallothionein ENSPM ENSPMT (15) T ENSF rsenite resistance 2 ENSPM ENSPMT (15) T ENSF alpain subunit calcium activated neutral proteinase canp ENSPM ENSPMT (2) T ENSF yclin t1 cyclin t cyct1 ENSPM ENSPMT (10) T ENSF Diaphanous related formin ENSPM ENSPMT (63) T T ENSF Dynein heavy chain ENSPM ENSPMT (3) T ENSF Peptidyl prolyl cis trans isomerase ppiase rotamase kda fkbp ENSPM ENSPMT (8) T ENSF Heterogeneous nuclear ribonucleoprotein m ENSPM ENSPMT (16) T ENSF Huntington's disease ENSPM ENSPMT (15) T ENSF Lethal 2 giant larvae ENSPM ENSPMT (19) T ENSF Lethal 2 giant larvae ENSPM ENSPMT (4) T ENSF Lipoyltransferase 1 mitochondrial precursor ec 6 lipoate ligase ENSPM ENSPMT (20) T ENSF Niemann pick c1 precursor ENSPM ENSPMT (15) T ENSF Phosphatidylinositol 4 5 bisphosphate 5 ENSPM ENSPMT (5) T ENSF Probable atp dependent rna helicase ENSPM ENSPMT (4) T ENSF Prohibitin b cell receptor associated ENSPM ENSPMT (3) T ENSF Retinal rod rhodopsin sensitive cgmp 3' 5' cyclic phosphodiesterase delta subunit ENSPM ENSPMT (3) T ENSF Ring finger 5 ENSPM ENSPMT (2) T ENSF Sarcoma amplified sequence homolog ENSPM ENSPMT (8) T ENSF Serine/threonine phosphatase 2a 55 kda regulatory subunit b

3 ENSPM ENSPMT (7) T ENSF Serine/threonine phosphatase ENSPM ENSPMT (2) T ENSF Signal recognition particle 68 kda srp68 ENSPM ENSPMT (11) T ENSF Sodium/hydrogen exchanger ENSPM ENSPMT (14) T ENSF Soluble adenylyl cyclase ENSPM ENSPMT (5) T ENSF Syntaxin 8 ENSPM ENSPMT (10) T ENSF T complex 1 subunit ENSPM ENSPMT (4) T ENSF Testis specific y encoded ENSPM ENSPMT (6) T ENSF Thioredoxin reductase ENSPM ENSPMT (13) T ENSF Transportin 1 importin beta 2 karyopherin beta 2 ENSPM ENSPMT (2) T ENSF Trna pseudouridine synthase a trna uridine isomerase i ENSPM ENSPMT (11) T ENSF Tyrosine phosphatase ENSPM ENSPMT (3) T ENSF snrna associated sm lsm8 ENSPM ENSPMT (1) T ENSF biquitin conjugating enzyme e2 h ENSPM ENSPMT , 15 (36) T ENSF Voltage gated calcium channel alpha subunit ENSPM ENSPMT (23) T ENSF Xanthine dehydrogenase ENSPM ENSPMT (6) T ENSF Zinc finger 207 ENSPM ENSPMT (5) T ENSF Zinc finger dhhc domain containing ENSPM ENSPMT (2) T ENSF Zinc finger zpr1 zinc finger 259 ENSPM ENSPMT (11) T ENSF mbiguous ENSPM ENSPMT (11) T ENSF mbiguous ENSPM ENSPMT (8) T ENSF mbiguous ENSPM ENSPMT (9) T ENSF mbiguous ENSPM ENSPMT (10) T ENSF mbiguous ENSPM ENSPMT (3) T ENSF mbiguous ENSPM ENSPMT (3) T ENSF mbiguous ENSPM ENSPMT (3) T ENSF mbiguous ENSPM ENSPMT (4) T ENSF mbiguous ENSPM ENSPMT (2) T ENSF nknown ENSPM ENSPMT (5) TT ENSF nknown ENSPM ENSPMT (2) T ENSF nknown ENSPM ENSPMT (2) T ENSF nknown ENSPM ENSPMT (4) T ENSF nknown ENSPM ENSPMT (11) T T ENSF nknown

4 *Because all Ensembl gene predictions are based on evidence derived from known protein, cdn, and EST sequences (urwen et al. 2004), in many cases genes are partially annotated. The positions of 12 introns presented in this table are based on number of exons that have been annotated for that transcript, and thus, do not necessarily reflect the position of 12 introns in the complete transcript. In parentheses the total number of introns inferred from annotated exons is presented. Reference Val urwen, Eduardo Eyras, T. Daniel ndrews, Laura larke, Emmanuel Mongin, Steven M.J. Searle, and Michele lamp The Ensembl utomatic ene nnotation System. enome Res. May; 14(5):

5 * - - * pis mellifera 1 snrn

6

7 * - - * - \ * \ \ \ \ \ \ \ \ / \ \ \ / / / / /

8 * - * * - -- pis mellifera 5 snrn

9 * - * - T - * * - -T pis mellifera u11 snrn

10 * - T T T T T - - * * - * - * pis mellifera 12 snrn

11

12 42 Dsim (3) - a Dmel 1:82Eb Dsim Dsec (2) - b 67 Dsec Dsim Dper Dmel (3), Dsim (1), Dsec (2), Dyak (8) - c 36 Dpse Dsim Dmel (1), Dsec (1) - d 38 Dsec Dsim Dpse (1), Dper (4) - e 45 Dpse (2) - f 56 Dyak Dpse Dpse (1), Dper (1) - g Dpse aeg aeg aeg aeg (2) - h aeg aeg aeg aeg gam gam gam (2) - i aeg gam (3) - j 29 gam aeg aeg aeg aeg aeg aeg aeg aeg mel mel mel mel mel Bmor Bmor Bmor Bmor Bmor Bmor Bmor Bmor Tcas Tcas (2) - k Tcas Tcas Figure S2.. Neighbor-joining tree of 1 snrn genes. Kimura two-parameter model with complete gap deletion, 157 sites, and 1000 bootstrap replicates were used to construct the tree. Labels: a - Dsim Dsim Dsim ; b - Dsec Dsec ; c - Dmel 1:21D Dmel 1:95b Dmel 1:95a Dsim Dsec Dsec Dyak Dyak Dyak Dyak Dyak Dyak Dyak Dyak ; d - Dmel 1:95c Dsec ; e - Dpse Dper Dper Dper Dper ; f - Dpse Dpse ; g - Dpse Dper ; h - aeg aeg ; i - gam gam ; j - gam gam gam ; k - Tcas Tcas

13 36 53 aeg aeg aeg aeg (5) - a aeg aeg gam gam (4) - b gam gam Dmel 2:14B Dmel (1), Dsec (3) - c 42 Dmel 2:38Bb Dsim Dsim (2) - d Dmel (2), Dsim (3), Dsec (3), Dyak (3) - e Dmel 2:34Ba Dpse (6), Dper (6) - f 46 Dpse Dpse Dper Dyak Dyak Dyak Dyak Bmor Bmor Bmor Bmor Bmor (3) - g 79 Bmor mel mel mel Tcas (3) - h 100 Tcas Figure S2.B. Neighbor-joining tree of 2 snrn genes. Kimura two-parameter model with complete gap deletion, 181 sites, and 1000 bootstrap replicates were used to construct the tree. Labels: a - aeg aeg aeg aeg aeg ; b - gam gam gam gam ; c - Dmel 2:38Ba Dsec Dsec Dsec ; d - Dsim Dsim ; e - Dmel 2:? Dmel 2:34Bb Dsim Dsim Dsim Dsec Dsec Dsec Dyak Dyak Dyak ; f - Dpse Dpse Dpse Dpse Dpse Dpse Dper Dper Dper Dper Dper Dper ; g - Bmor Bmor Bmor ; h - Tcas Tcas Tcas

14 50 aeg gam aeg aeg Dmel (1), Dsim (1), Dsec (1) - a 100 Dyak Dper Dmel (1), Dsec (1), Dyak (1) - b Dsim Dpse (1), Dper (1) - c Dmel (1), Dsim (1), Dsec (1) - d Dyak Dpse (1), Dper (1) - e Bmor Bmor Bmor mel mel Tcas Tcas Figure S2.. Neighbor-joining tree of 4 snrn genes. Kimura two-parameter model with complete gap deletion, 139 sites, and 1000 bootstrap replicates were used to construct the tree. Labels: a - Dmel 4:25F Dsim Dsec ; b - Dmel 4:39B Dsec Dyak ; c - Dpse Dper ; d - Dmel 4:38B Dsim Dsec ; e - Dpse Dper