Two Eel Scaffolds

Introduction

Two DNA scaffolds are presented:

1. eelScaffold32. 679 422 bp and 42.25% GC.
2. eelScaffold320. 246 433 bp and 43.47% GC.

We take tilapia (Oreochromis niloticus, Ensembl abbreviation ONI) to be the reference.

There are two genes expected to be around about the regions covered by these scaffolds:

• eelScaffold32 contains any part of PDCD10b (Programmed cell death 10b).
• eelScaffold320 contains any part of nrd1a (Nardilysin, N-arginine dibasic convertase)

Gene Predictor

One of the most up-to-date (2016) gene predictors is Augustus. It uses HMM profiles based on a related organism. In terms of eel, there are two given organisms: Zebra fish (zb) and Lamprey (lp) which Augustus makes available. Though tilapia is not available, it is possible - given time - to train and establish HMM profile for this organism.

An example Augustus command line is as follows:

augustus --species=lamprey eelScaffold320.fa >aug_s320_lp.gtf

Augustus outputs in the GTF format, for visual browsing on JBrowse, we need to convert to the related format, GFF:

gtf2gff.pl --printExon --gff3 < aug_s32_lp.gtf --out=aug_s32_lp.gff

We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the follown Augustus-supplied script:

getAnnoFasta.pl --seqfile=eelScaffold32.fa aug_s32_lp.gtf

In order to visually navigate the results of these annotations, they can be viewed on a browser here.

Detecting presence of pdcd10b and nrd1a

We obtain these genes from the tilapia and then their exons and apply Smith-Waterman alignment (via the Emboss program, wrapped in script with the scaffolds to them. We order via scaffold starting site (reverse strand end site).

pdcd10b's 7 exons against eelScaffold32

Output of script:

SFI ALEN SCORE IDEN IPT SIM GAPS GPT TSC TEC PET QSC QEC QLN PEQ 5 89 125.5 56 62.9 56 15 16.9 92493 92577 0.0 1 78 79 98.7 7 80 112.0 52 65.0 52 16 20.0 153839 153911 0.0 1 71 82 86.6 6 97 113.0 59 60.8 59 20 20.6 222386 222481 0.0 4 81 83 94.0 2 54 105.0 37 68.5 37 7 13.0 270271 270324 0.0 2 48 54 87.0 1 91 134.0 58 63.7 58 9 9.9 305491 305572 0.0 6 96 96 94.8 4 149 161.5 91 61.1 91 29 19.5 337277 337419 0.0 2 127 127 99.2 3 112 129.5 69 61.6 69 16 14.3 607211 607313 0.0 7 111 118 89.0 Score for 7 query sequences (total 639 bp) against forward-sense target (679422 bp) = 880.50 SFI ALEN SCORE IDEN IPT SIM GAPS GPT TSC TEC PET QSC QEC QLN PEQ 7 82 320.0 72 87.8 72 0 0.0 441200 441281 0.0 1 82 82 100.0 6 83 334.0 74 89.2 74 0 0.0 442739 442821 0.0 1 83 83 100.0 5 78 282.0 66 84.6 66 0 0.0 442964 443041 0.0 1 78 79 98.7 4 127 437.0 105 82.7 105 0 0.0 443355 443481 0.0 1 127 127 100.0 3 51 183.0 43 84.3 43 0 0.0 445730 445780 0.0 1 51 118 43.2 2 54 198.0 46 85.2 46 0 0.0 446360 446413 0.0 1 54 54 100.0 1 94 380.0 84 89.4 84 0 0.0 448216 448309 0.0 3 96 96 97.9 Score for 7 query sequences (total 639 bp) against reverse-sense target (679422 bp) = 2134.00 Key: SFI src file idx, ALEN aln length, SCORE aln score, IDEN identical bases, IPT percent iden, SIM similar bases, GAPS num gaps, GPT gap percent

       TSC target start query, TEC target end coord, PET percent of target, QSC Query start coord, QEC query end coord, QLN query aln length, PEQ percent of query

We can clearly see good alignment on the reverse strand, and so can verify pdcd10b presence in eelScaffold32.

pdcd10b discussion

This is a small gene, however we cannot say these alignments are conclusive. It is clear however that eelScaffold32 has a higher probability of harbouring pdcd10b.

nrd1a's 37 exons against eelScaffold32

SFI ALEN SCORE IDEN IPT SIM GAPS GPT TSC TEC PET QSC QEC QLN PEQ 32 52 99.5 36 69.2 36 4 7.7 11214 11261 0.0 10 61 84 61.9 18 46 105.5 34 73.9 34 4 8.7 21678 21720 0.0 1 45 55 81.8 17 70 95.0 45 64.3 45 20 28.6 22625 22693 0.0 3 53 59 86.4 24 40 96.5 29 72.5 29 2 5.0 22849 22886 0.0 8 47 52 76.9 23 21 69.0 17 81.0 17 0 0.0 26374 26394 0.0 1 21 22 95.5 6 18 72.0 16 88.9 16 0 0.0 28762 28779 0.0 5 22 23 78.3 14 64 105.5 42 65.6 42 9 14.1 42560 42621 0.0 12 68 70 81.4 2 315 228.0 183 58.1 183 64 20.3 46282 46552 0.1 7 301 324 91.0 21 90 112.5 58 64.4 58 17 18.9 80763 80842 0.0 3 85 87 95.4 25 153 138.0 88 57.5 88 27 17.6 81195 81324 0.1 1 149 151 98.7 11 81 148.5 55 67.9 55 10 12.3 81550 81625 0.0 47 122 123 61.8 1 525 261.0 294 56.0 294 105 20.0 83281 83764 0.2 2 462 541 85.2 15 61 107.0 40 65.6 40 4 6.6 89643 89699 0.0 8 68 78 78.2 28 39 78.0 28 71.8 28 8 20.5 92398 92435 0.0 1 32 32 100.0 8 168 147.0 104 61.9 104 32 19.0 97584 97741 0.1 8 153 154 94.8 3 254 229.0 150 59.1 150 55 21.7 106270 106501 0.1 6 226 241 91.7 31 54 88.5 37 68.5 37 6 11.1 106293 106342 0.0 2 53 53 98.1 29 129 142.5 79 61.2 79 30 23.3 107213 107332 0.0 23 130 139 77.7 13 70 119.0 46 65.7 46 5 7.1 108538 108605 0.0 1 67 74 90.5 4 37 84.5 27 73.0 27 3 8.1 129499 129534 0.0 3 37 38 92.1 37 131 128.5 79 60.3 79 26 19.8 133637 133753 0.0 13 131 131 90.8 35 96 114.5 60 62.5 60 21 21.9 135814 135897 0.0 1 87 90 96.7 9 78 106.5 50 64.1 50 14 17.9 136915 136989 0.0 5 71 74 90.5 30 39 87.0 27 69.2 27 0 0.0 137258 137296 0.0 1 39 48 81.2 22 114 120.0 69 60.5 69 20 17.5 143789 143896 0.0 2 101 101 99.0 5 30 64.5 22 73.3 22 6 20.0 158927 158955 0.0 1 25 26 96.2 27 176 145.0 102 58.0 102 39 22.2 161163 161325 0.1 13 162 163 92.0 33 89 109.0 56 62.9 56 19 21.3 164489 164570 0.0 5 81 91 84.6 10 82 119.0 52 63.4 52 11 13.4 168702 168776 0.0 1 78 96 81.2 7 81 106.5 50 61.7 50 7 8.6 178661 178740 0.0 4 78 82 91.5 20 121 141.5 76 62.8 76 21 17.4 178727 178838 0.0 14 122 124 87.9 12 43 98.0 31 72.1 31 4 9.3 202832 202872 0.0 5 45 58 70.7 36 65 118.0 44 67.7 44 8 12.3 208219 208279 0.0 3 63 70 87.1 19 120 157.5 76 63.3 76 29 24.2 221343 221456 0.0 2 98 105 92.4 34 86 124.0 58 67.4 58 14 16.3 221411 221484 0.0 19 102 117 71.8 26 123 127.5 74 60.2 74 14 11.4 225229 225348 0.0 4 115 128 87.5 16 129 126.0 77 59.7 77 21 16.3 226946 227071 0.1 11 121 121 91.7 Score for 37 query sequences (total 4025 bp) against forward-sense target (246433 bp) = 4519.50 SFI ALEN SCORE IDEN IPT SIM GAPS GPT TSC TEC PET QSC QEC QLN PEQ 36 79 135.5 53 67.1 53 13 16.5 31943 31868 0.0 2 70 70 98.6 1 531 279.0 295 55.6 295 122 23.0 45314 44814 0.2 52 490 541 81.1 37 130 317.0 93 71.5 93 0 0.0 89006 88877 0.1 1 130 131 99.2 35 91 213.5 66 72.5 66 4 4.4 89289 89201 0.0 1 89 90 98.9 34 117 360.0 92 78.6 92 0 0.0 89570 89454 0.0 1 117 117 100.0 33 93 249.0 70 75.3 70 4 4.3 89661 89571 0.0 1 91 91 100.0 32 82 275.0 67 81.7 67 0 0.0 90249 90168 0.0 2 83 84 97.6 31 53 211.0 47 88.7 47 0 0.0 90460 90408 0.0 1 53 53 100.0 30 48 123.0 35 72.9 35 0 0.0 91371 91324 0.0 1 48 48 100.0 29 140 422.5 111 79.3 111 4 2.9 92104 91967 0.1 2 139 139 99.3 28 32 97.0 25 78.1 25 0 0.0 92269 92238 0.0 1 32 32 100.0 26 118 365.0 93 78.8 93 0 0.0 93668 93551 0.0 11 128 128 92.2 25 150 408.0 113 75.3 113 4 2.7 94026 93879 0.1 3 150 151 98.0 24 52 107.0 35 67.3 35 0 0.0 94307 94256 0.0 1 52 52 100.0 22 101 253.0 73 72.3 73 0 0.0 94586 94486 0.0 1 101 101 100.0 21 89 185.5 62 69.7 62 4 4.5 94810 94724 0.0 1 87 87 100.0 20 124 359.0 95 76.6 95 0 0.0 95025 94902 0.1 1 124 124 100.0 19 101 289.0 77 76.2 77 0 0.0 95301 95201 0.0 4 104 105 96.2 18 53 202.0 46 86.8 46 0 0.0 96070 96018 0.0 2 54 55 96.4 17 59 214.0 50 84.7 50 0 0.0 96407 96349 0.0 1 59 59 100.0 16 123 426.0 103 83.7 103 4 3.3 96984 96864 0.0 1 121 121 100.0 15 77 286.0 66 85.7 66 0 0.0 97271 97195 0.0 1 77 78 98.7 14 67 200.0 52 77.6 52 0 0.0 97698 97632 0.0 4 70 70 95.7 13 74 181.0 53 71.6 53 0 0.0 98226 98153 0.0 1 74 74 100.0 12 58 227.0 51 87.9 51 0 0.0 98381 98324 0.0 1 58 58 100.0 11 124 284.0 88 71.0 88 2 1.6 98767 98645 0.0 1 123 123 100.0 10 96 336.0 80 83.3 80 0 0.0 99168 99073 0.0 1 96 96 100.0 9 73 239.0 59 80.8 59 0 0.0 99376 99304 0.0 2 74 74 98.6 8 155 583.0 135 87.1 135 2 1.3 99775 99622 0.1 1 154 154 100.0 7 83 205.0 61 73.5 61 2 2.4 100033 99952 0.0 1 82 82 100.0 3 255 397.5 169 66.3 169 31 12.2 100943 100706 0.1 1 241 241 100.0 2 331 330.5 196 59.2 196 57 17.2 101996 101708 0.1 9 324 324 97.5 6 21 63.0 17 81.0 17 1 4.8 113266 113247 0.0 2 22 23 91.3 5 25 71.0 21 84.0 21 3 12.0 141681 141659 0.0 2 25 26 92.3 27 171 165.0 104 60.8 104 37 21.6 142906 142741 0.1 18 156 163 85.3 23 22 78.5 19 86.4 19 2 9.1 213180 213159 0.0 2 21 22 90.9 4 46 92.0 31 67.4 31 8 17.4 228513 228468 0.0 1 38 38 100.0 Score for 37 query sequences (total 4025 bp) against reverse-sense target (246433 bp) = 9229.50

Thisis a more complicated gene, leading to ore

nrd1a discussion

Also an inconclusive analysis. EelScaffold32 again is more likely to be harbouring this second gene. Being some three time longer, it has a higher prior likelihood for this.