Based on the DNA sequences, most of the trnas could be folded as cloverleaf

Transcription

1 Putative secondary structures of trnas Based on the DNA sequences, most of the trnas could be folded as cloverleaf secondary structures. A few of them possessed nonwatsoncrick matches, aberrant loops, or even extremely short arms. Most of the trnas (GCT) lost their DHU arms, which is not rare in insect mtgenomes. In some cases, the alternative folding could yield a structure with an extremely short DHU stem and a small loop. It has been supposed that these characteristics in mtgenome are partly because the mtdna was not subject to the process of recombination, which may facilitate the elimination of deleterious mutations [1]. However, recombination in insect mtdna has been observed [2]. It is not known whether the aberrant trnas lose their function in every case, but there are reports of the recruitment of nuclear trnas into the mitochondria [3, 4], and a type of RNA editing could recover the wellpaired acceptor stem [5].

2 Figure 1 Putative secondary structures of mitochondrial trna molecules from Aphelocheiridae

3 Figure 2 Putative secondary structures of mitochondrial trna molecules from Belostomatidae

4 Figure 3 Putative secondary structures of mitochondrial trna molecules from Corixidae

5 Figure 4 Putative secondary structures of mitochondrial trna molecules from Fulgoridae

6 Figure 5 Putative secondary structures of mitochondrial trna molecules from Gelastocoridae

7 Figure 6 Putative secondary structures of mitochondrial trna molecules from Gerridae

8 Figure 7 Putative secondary structures of mitochondrial trna molecules from Hydrometridae

9 Figure 8 Putative secondary structures of mitochondrial trna molecules from Leptopodidae

10 Figure 9 Putative secondary structures of mitochondrial trna molecules from Naucoridae

11 Figure 10 Putative secondary structures of mitochondrial trna molecules from Nepidae

12 Figure 11 Putative secondary structures of mitochondrial trna molecules from Notonectidae

13 Figure 12 Putative secondary structures of mitochondrial trna molecules from Ochteridae

14 Figure 13 Putative secondary structures of mitochondrial trna molecules from Pleidae

15 Figure 14 Putative secondary structures of mitochondrial trna molecules from Reduviidae * indicated the G=U match.

16 Codon usage of protein coding genes The most frequent codons do not always correspond with their cognates in the mitochondrial trnas. It appears that the recognition of the cognates between the anticodons and the codons is not related to translation efficiency. Furthermore, the most infrequently used fourfold degenerate codons are NNG and the most frequently used codons are NNA. Table 1 Condon Usage of Aphelocheiridae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

17 Table 2 Condon Usage of Belostomatidae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

18 Table 3 Condon Usage of Corixidae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

19 Table 4 Condon Usage of Fulgoridae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

20 Table 5 Condon Usage of Gelastocoridae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

21 Table 6 Condon Usage of Gerridae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

22 Table 7 Condon Usage of Hydrometridae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

23 Table 8 Condon Usage of Leptopodidae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

24 Table 9 Condon Usage of Naucoridae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

25 Table 10 Condon Usage of Nepidae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

26 Table 11 Condon Usage of Notonectidae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

27 Table 12 Condon Usage of Ochteridae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

28 Table 13 Condon Usage of Pleidae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG

29 Table 14 Condon Usage of Reduviidae Phe UUU Ser UCU UUC UCC Leu UUA UCA UUG UCG CUU Pro CCU CUC CCC CUA CCA CUG CCG Ile AUU Thr ACU AUC ACC Met AUA ACA AUG ACG Val GUU Ala GCU GUC GCC GUA GCA GUG GCG Tyr UAU Cys UGU UAC UGC TER UAA Trp UGA UAG UGG His CAU Arg CGU CAC CGC Gln CAA CGA CAG CGG Asn AAU Ser AGU AAC AGC Lys AAA AGA AAG AGG Asp GAU Gly GGU GAC GGC Glu GAA GGA GAG GGG TER, stop codon (single T stop codon was not included in this talbe); RSCU, relative synonymous codon usage; n *, total number in double strands; RSCU *, RSCU in double strands; n, total number in the plus strand; RSCU, RSCU in the plus strand; n, total number in the minus strand; RSCU, RSCU in the minus strand.

30 Nucleotide composition Among the mtgenomes sequenced in this study, the nucleotide compositions are biased toward adenines and thymines. The nucleotide skew statistics of Jstrands indicate that the heteropterans are ATskewed and CGskewed. Although several mtgenomes are not completely sequenced, these skew trends are obvious. Table 15 Nucleotide composition of Aphelocheiridae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 16 Nucleotide composition of Belostomatidae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control

31 Table 17 Nucleotide composition of Corixidae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 18 Nucleotide composition of Fulgoridae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 19 Nucleotide composition of Gelastocoridae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control

32 Table 20 Nucleotide composition of Gerridae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 21 Nucleotide composition of Hydrometridae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 22 Nucleotide composition of Leptopodidae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control

33 Table 23 Nucleotide composition of Naucoridae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 24 Nucleotide composition of Nepidae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 25 Nucleotide composition of Notonectidae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control

34 Table 26 Nucleotide composition of Ochteridae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 27 Nucleotide composition of Pleidae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control Table 28 Nucleotide composition of Reduviidae Length(bp) A% G% C% T% AT % ATskew CGskew Whole_J PCGs PCGs_J PCGs_N trnas trnas_j trnas_n rrnas Control References 1. Lynch M: Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes. Mol Biol Evol 1997, 14: Tsaousis AD, Martin DP, Ladoukakis ED, Posada D, Zouros E: Widespread recombination in published animal mtdna sequences. Mol Biol Evol 2005, 22:

35 3. Adams KL, Palmer JD: Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 2003, 29: Podsiadlowski L, Braband A: The complete mitochondrial genome of the sea spider Nymphon gracile (Arthropoda: Pycnogonida). BMC Genomics 2006, 7: Lavrov DV, Brown WM, Boore JL: A novel type of RNA editing occurs in the mitochondrial trnas of the centipede Lithobius forficatus. Proc Natl Acad Sci U S A 2000, 97: