%PDF-1.6
%
1 0 obj
<>
endobj
2 0 obj
<>stream
Luc Cornet, Loïc Meunier, Mick Van Vlierberghe, Raphaël R. Léonard, Benoit Durieu, Yannick Lara, Agnieszka Misztak, Damien Sirjacobs, Emmanuelle J. Javaux, Hervé Philippe, Annick Wilmotte, Denis Baurain
Consensus assessment of the contamination level of publicly available cyanobacterial genomes
www.plosone.org
www.plosone.org
endstream
endobj
3 0 obj
<>/XObject<>>>/CropBox[0 0 612 792]/MediaBox[0 0 612 792]/Parent 11 0 R/Annots 12 0 R/Contents 13 0 R/TrimBox[0 0 612 792]>>
endobj
12 0 obj
[14 0 R 15 0 R 16 0 R 17 0 R 18 0 R 19 0 R 20 0 R 21 0 R 22 0 R 23 0 R 24 0 R 25 0 R 26 0 R 27 0 R 28 0 R 29 0 R 30 0 R 31 0 R 32 0 R 33 0 R 34 0 R 35 0 R 36 0 R 37 0 R 38 0 R 39 0 R 40 0 R 41 0 R 42 0 R]
endobj
14 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref001)>>
endobj
15 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref003)>>
endobj
16 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref004)>>
endobj
17 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref005)>>
endobj
18 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref006)>>
endobj
19 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref005)>>
endobj
20 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref007)>>
endobj
21 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref008)>>
endobj
22 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref009)>>
endobj
23 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref010)>>
endobj
24 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref005)>>
endobj
25 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref011)>>
endobj
26 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref012)>>
endobj
27 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref013)>>
endobj
28 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref002)>>
endobj
29 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref001)>>
endobj
30 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref014)>>
endobj
31 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref015)>>
endobj
32 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref016)>>
endobj
33 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref014)>>
endobj
34 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref003)>>
endobj
35 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref017)>>
endobj
36 0 obj
<>/Border[0 0 0]/A 43 0 R>>
endobj
43 0 obj
<>
endobj
37 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref018)>>
endobj
38 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref019)>>
endobj
39 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref013)>>
endobj
40 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref020)>>
endobj
41 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref022)>>
endobj
42 0 obj
<>/Border[0 0 0]/A 44 0 R>>
endobj
44 0 obj
<>
endobj
13 0 obj
[45 0 R 46 0 R 47 0 R 48 0 R 49 0 R 50 0 R 51 0 R 52 0 R 53 0 R 54 0 R 55 0 R 56 0 R 57 0 R 58 0 R 59 0 R 60 0 R 61 0 R 62 0 R 63 0 R 64 0 R 65 0 R 66 0 R]
endobj
45 0 obj
<>stream
q
0.83 0.64 0.02 0 k
421.7386 693.2976 m
426.4441 693.2976 l
h
f*
431.5465 693.2976 m
436.252 693.2976 l
h
f*
558.4252 667.3323 m
563.074 667.3323 l
h
f*
565.285 667.3323 m
569.9906 667.3323 l
h
f*
448.8945 654.3496 m
453.6 654.3496 l
h
f*
445.2661 641.3102 m
449.915 641.3102 l
h
f*
364.8189 615.3449 m
369.5244 615.3449 l
h
f*
493.2283 602.3055 m
497.9339 602.3055 l
h
f*
285.5055 589.3228 m
290.211 589.3228 l
h
f*
474.0661 576.3402 m
483.4205 576.3402 l
h
f*
275.5276 550.3181 m
280.2898 550.3181 l
h
f*
282.5575 550.3181 m
292.0819 550.3181 l
h
f*
294.3496 550.3181 m
303.8173 550.3181 l
h
f*
422.7591 537.3354 m
432.2835 537.3354 l
h
f*
417.7701 511.3134 m
422.5323 511.3134 l
h
f*
314.5323 498.3307 m
319.2945 498.3307 l
h
f*
366.9732 498.3307 m
376.4976 498.3307 l
h
f*
427.2378 498.3307 m
436.7622 498.3307 l
h
f*
468.2835 498.3307 m
477.8079 498.3307 l
h
f*
311.7543 485.348 m
321.2787 485.348 l
h
f*
376.2142 446.3433 m
380.9764 446.3433 l
h
f*
383.2441 446.3433 m
392.7685 446.3433 l
h
f*
227.8488 329.3291 m
387.6661 329.3291 l
h
f*
267.5339 290.3244 m
277.0016 290.3244 l
h
f*
445.4929 160.3276 m
455.0173 160.3276 l
h
f*
271.1622 134.3055 m
280.4031 134.3055 l
h
f*
454.1102 95.3008 m
463.3512 95.3008 l
h
f*
468.3402 95.3008 m
477.5811 95.3008 l
h
f*
0 g
1 j
1 J
0 w
10 0 0 10 200.0125 707.4141 cm
BT
/F7 1 Tf
1 TL
-0.01 Tc
0 0 Td
(structural)Tj
4.0195 0 Td
(and)Tj
1.7121 0 Td
(functional)Tj
4.2462 0 Td
(annotation,)Tj
4.7736 0 Td
(contamination)Tj
6.0434 0 Td
(level\))Tj
2.3187 0 Td
(is)Tj
0.8334 0 Td
(thus)Tj
1.9105 0 Td
(of)Tj
1.0035 0 Td
(primary)Tj
3.4129 0 Td
(importance.)Tj
4.9946 0 Td
(Com-)Tj
-35.2684 -1.3039 Td
(pleteness)Tj
3.77 0 Td
(and)Tj
1.7121 0 Td
(annotation)Tj
4.5468 0 Td
(have)Tj
2.0409 0 Td
(attracted)Tj
3.6737 0 Td
(some)Tj
2.3074 0 Td
(attention)Tj
3.787 0 Td
([)Tj
0.83 0.64 0.02 0 k
(1)Tj
0 g
()Tj
0.83 0.64 0.02 0 k
(3)Tj
0 g
(])Tj
2.3414 0 Td
(but,)Tj
1.7518 0 Td
(surprisingly,)Tj
5.1307 0 Td
(the)Tj
1.4513 0 Td
(issue)Tj
2.126 0 Td
(of)Tj
1.0035 0 Td
(con-)Tj
-35.6426 -1.2982 Td
(taminating)Tj
4.541 0 Td
(sequences)Tj
4.1613 0 Td
(has)Tj
1.525 0 Td
(remained)Tj
3.9911 0 Td
(untackled)Tj
4.0932 0 Td
(at)Tj
0.9355 0 Td
(large)Tj
2.1316 0 Td
(scale)Tj
2.0806 0 Td
(\(i.e.,)Tj
1.8879 0 Td
(for)Tj
1.372 0 Td
(a)Tj
0.6462 0 Td
(whole)Tj
2.5796 0 Td
(phylum\),)Tj
3.8324 0 Td
(despite)Tj
-33.7774 -1.2983 Td
(the)Tj
1.4513 0 Td
(well)Tj
1.7971 0 Td
(known)Tj
2.9707 0 Td
(evidence)Tj
3.668 0 Td
(that)Tj
1.7518 0 Td
(contaminants)Tj
5.6353 0 Td
(are)Tj
1.4343 0 Td
(frequently)Tj
4.2463 0 Td
(introduced)Tj
4.5864 0 Td
(during)Tj
2.8913 0 Td
(experiments)Tj
5.074 0 Td
([)Tj
0.83 0.64 0.02 0 k
(4)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(5)Tj
0 g
(])Tj
-35.5065 -1.2983 Td
(or)Tj
1.0828 0 Td
(stem)Tj
2.1033 0 Td
(from)Tj
2.177 0 Td
(natural)Tj
3.0387 0 Td
(associations)Tj
4.9209 0 Td
(and)Tj
1.7121 0 Td
(insufficient)Tj
4.6545 0 Td
(purification)Tj
4.8642 0 Td
([)Tj
0.83 0.64 0.02 0 k
(6)Tj
0 g
(].)Tj
1.5817 0 Td
(Overlooked)Tj
4.8642 0 Td
(contaminants)Tj
-30.9994 -1.3039 Td
(may)Tj
1.9105 0 Td
(have)Tj
2.0353 0 Td
(major)Tj
2.5795 0 Td
(detrimental)Tj
4.8132 0 Td
(effects)Tj
2.6815 0 Td
(on)Tj
1.2643 0 Td
(biological)Tj
4.0308 0 Td
(conclusions)Tj
4.8756 0 Td
([)Tj
0.83 0.64 0.02 0 k
(5)Tj
0 g
(].)Tj
1.576 0 Td
(For)Tj
1.6101 0 Td
(instance,)Tj
3.6907 0 Td
(the)Tj
1.457 0 Td
(disappear-)Tj
-32.5245 -1.2982 Td
(ance)Tj
2.0239 0 Td
(of)Tj
1.0034 0 Td
(two)Tj
1.6895 0 Td
(well-accepted)Tj
5.5672 0 Td
(monophyletic)Tj
5.6862 0 Td
(clades)Tj
2.6022 0 Td
(of)Tj
1.0035 0 Td
(charophycean)Tj
5.7373 0 Td
(green)Tj
2.4264 0 Td
(algae)Tj
2.1884 0 Td
(\(Coleochaetales)Tj
-29.928 -1.2983 Td
(and)Tj
1.7007 0 Td
(Zygnematales\))Tj
5.9811 0 Td
(was)Tj
1.6724 0 Td
(initially)Tj
3.1861 0 Td
(reported)Tj
3.6057 0 Td
([)Tj
0.83 0.64 0.02 0 k
(7)Tj
0 g
(],)Tj
1.5647 0 Td
(but)Tj
1.525 0 Td
(later)Tj
1.9559 0 Td
(revealed)Tj
3.4696 0 Td
(to)Tj
1.0035 0 Td
(be)Tj
1.1282 0 Td
(due)Tj
1.6724 0 Td
(to)Tj
1.0034 0 Td
(cross-contaminating)Tj
-29.4687 -1.3039 Td
(sequences)Tj
4.1555 0 Td
(in)Tj
1.0205 0 Td
(the)Tj
1.4456 0 Td
(dataset)Tj
2.9481 0 Td
(made)Tj
2.398 0 Td
(of)Tj
0.9978 0 Td
(transcriptomes)Tj
6.1285 0 Td
(of)Tj
0.9978 0 Td
(green)Tj
2.4151 0 Td
(algae)Tj
2.1883 0 Td
(and)Tj
1.7065 0 Td
(plants)Tj
2.5852 0 Td
([)Tj
0.83 0.64 0.02 0 k
(8)Tj
0 g
(].)Tj
1.5703 0 Td
(Similarly,)Tj
3.9628 0 Td
(another)Tj
-34.52 -1.2983 Td
(phylogenomic)Tj
5.8563 0 Td
(study)Tj
2.3584 0 Td
([)Tj
0.83 0.64 0.02 0 k
(9)Tj
0 g
(])Tj
1.355 0 Td
(wrongly)Tj
3.4582 0 Td
(concluded)Tj
4.32 0 Td
(to)Tj
1.0148 0 Td
(a)Tj
0.6463 0 Td
(basal)Tj
2.1713 0 Td
(emergence)Tj
4.49 0 Td
(of)Tj
1.0035 0 Td
(bilaterian)Tj
3.9571 0 Td
(animals,)Tj
3.5093 0 Td
(owing)Tj
-34.1402 -1.2983 Td
(to)Tj
1.0147 0 Td
(a)Tj
0.6463 0 Td
(combination)Tj
5.2781 0 Td
(of)Tj
1.0035 0 Td
(contamination)Tj
6.0434 0 Td
(and)Tj
1.7121 0 Td
(taxonomic)Tj
4.439 0 Td
(misidentification)Tj
6.9335 0 Td
([)Tj
0.83 0.64 0.02 0 k
(10)Tj
0 g
(].)Tj
-0.004 Tc
-25.8744 -1.3039 Td
(In)Tj
1.1111 0 Td
(practice,)Tj
3.6057 0 Td
(contaminants)Tj
5.7089 0 Td
(arise)Tj
2.075 0 Td
(at)Tj
0.9524 0 Td
(different)Tj
3.6567 0 Td
(steps,)Tj
2.4037 0 Td
(from)Tj
2.2054 0 Td
(sampling)Tj
3.8834 0 Td
(to)Tj
1.0205 0 Td
(sequencing,)Tj
4.9436 0 Td
(and)Tj
1.7291 0 Td
(any-)Tj
-34.4917 -1.2982 Td
(where)Tj
2.6475 0 Td
(in)Tj
1.0375 0 Td
(between)Tj
3.5262 0 Td
([)Tj
0.83 0.64 0.02 0 k
(5)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(11)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(12)Tj
0 g
(].)Tj
3.9572 0 Td
(Yet,)Tj
1.7971 0 Td
(for)Tj
1.389 0 Td
(many)Tj
2.4775 0 Td
(\(microbial\))Tj
4.7395 0 Td
(organisms,)Tj
4.5807 0 Td
(an)Tj
1.2019 0 Td
(aggravating)Tj
4.8586 0 Td
(factor)Tj
2.5398 0 Td
(is)Tj
0.8504 0 Td
(the)Tj
-35.6029 -1.2983 Td
(difficulty)Tj
3.8097 0 Td
(to)Tj
1.0205 0 Td
(obtain)Tj
2.7836 0 Td
(and)Tj
1.7291 0 Td
(keep)Tj
2.0806 0 Td
(axenic)Tj
2.7836 0 Td
(\(i.e.,)Tj
1.9276 0 Td
(pure\))Tj
2.398 0 Td
(cultures)Tj
3.4016 0 Td
([)Tj
0.83 0.64 0.02 0 k
(13)Tj
0 g
(],)Tj
2.0749 0 Td
(explaining)Tj
4.4051 0 Td
(why)Tj
1.8878 0 Td
(a)Tj
0.652 0 Td
(number)Tj
3.4185 0 Td
(of)Tj
-34.3726 -1.3039 Td
(sequenced)Tj
4.3823 0 Td
(microbial)Tj
4.0648 0 Td
(strains)Tj
2.863 0 Td
(are)Tj
1.4457 0 Td
(not)Tj
1.576 0 Td
(devoid)Tj
2.9254 0 Td
(of)Tj
1.0148 0 Td
(contaminants.)Tj
5.9357 0 Td
(While)Tj
2.6475 0 Td
(some)Tj
2.3357 0 Td
(tools)Tj
2.1374 0 Td
(can)Tj
1.627 0 Td
(assess)Tj
2.5172 0 Td
(the)Tj
-35.4725 -1.2983 Td
(technical)Tj
3.8097 0 Td
(quality)Tj
2.9537 0 Td
(of)Tj
1.0148 0 Td
(genome)Tj
3.4129 0 Td
(assemblies)Tj
4.422 0 Td
(\(e.g.,)Tj
2.126 0 Td
(QUAST,)Tj
3.6963 0 Td
([)Tj
0.83 0.64 0.02 0 k
(2)Tj
0 g
(]\),)Tj
1.9446 0 Td
(or)Tj
1.0941 0 Td
(their)Tj
2.109 0 Td
(completeness)Tj
5.5729 0 Td
(in)Tj
1.0374 0 Td
(terms)Tj
2.4945 0 Td
(of)Tj
-35.6879 -1.2982 Td
(gene)Tj
2.0749 0 Td
(content)Tj
3.2712 0 Td
(\(e.g.,)Tj
2.1203 0 Td
(BUSCO,)Tj
3.6453 0 Td
([)Tj
0.83 0.64 0.02 0 k
(1)Tj
0 g
(],)Tj
1.5987 0 Td
(CheckM)Tj
3.6454 0 Td
([)Tj
0.83 0.64 0.02 0 k
(14)Tj
0 g
(],)Tj
2.0749 0 Td
(ProDeGe)Tj
3.9515 0 Td
([)Tj
0.83 0.64 0.02 0 k
(15)Tj
0 g
(],)Tj
2.0749 0 Td
(acdc)Tj
2.0296 0 Td
([)Tj
0.83 0.64 0.02 0 k
(16)Tj
0 g
(]\))Tj
2.1883 0 Td
(or)Tj
1.0942 0 Td
(even)Tj
2.0693 0 Td
(their)Tj
2.109 0 Td
(contami-)Tj
-33.9475 -1.2983 Td
(nation)Tj
2.8232 0 Td
(level)Tj
2.0126 0 Td
(\(e.g.,)Tj
2.126 0 Td
(CheckM,)Tj
3.8721 0 Td
([)Tj
0.83 0.64 0.02 0 k
(14)Tj
0 g
(]\),)Tj
2.4151 0 Td
(bioinformatic)Tj
5.7259 0 Td
(procedures)Tj
4.6772 0 Td
(are)Tj
1.4456 0 Td
(still)Tj
1.6385 0 Td
(needed)Tj
3.0954 0 Td
(to)Tj
1.0261 0 Td
(recognize)Tj
4.0649 0 Td
(and)Tj
-34.9226 -1.3039 Td
(eliminate)Tj
3.9458 0 Td
(the)Tj
1.4683 0 Td
(contaminating)Tj
6.0831 0 Td
(sequences.)Tj
-10.301 -1.2983 Td
(As)Tj
1.2699 0 Td
(their)Tj
2.1033 0 Td
(efficiency)Tj
4.0308 0 Td
(ultimately)Tj
4.2349 0 Td
(depends)Tj
3.549 0 Td
(on)Tj
1.2756 0 Td
(the)Tj
1.4683 0 Td
(quality)Tj
2.9594 0 Td
(and)Tj
1.7291 0 Td
(representativity)Tj
6.4289 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.474 0 Td
(reference)Tj
-32.7342 -1.2983 Td
(databases)Tj
3.9968 0 Td
(used)Tj
2.0636 0 Td
(for)Tj
1.3833 0 Td
(taxonomic)Tj
4.49 0 Td
(classification)Tj
5.3461 0 Td
([)Tj
0.83 0.64 0.02 0 k
(3)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(17)Tj
0 g
(],)Tj
2.778 0 Td
(the)Tj
1.4683 0 Td
(identification)Tj
5.5899 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4683 0 Td
(genome)Tj
3.4073 0 Td
(regions)Tj
-33.0064 -1.3039 Td
(contaminated)Tj
5.7486 0 Td
(by)Tj
1.1792 0 Td
(foreign)Tj
3.0954 0 Td
(sequences)Tj
4.2179 0 Td
(\(and)Tj
2.0693 0 Td
(their)Tj
2.109 0 Td
(elimination\))Tj
5.1873 0 Td
(is)Tj
0.8447 0 Td
(an)Tj
1.2076 0 Td
(important)Tj
4.2803 0 Td
(endeavor,)Tj
4.1329 0 Td
(both)Tj
2.0636 0 Td
(to)Tj
-36.1358 -1.2982 Td
(avoid)Tj
2.4094 0 Td
(wrong)Tj
2.7949 0 Td
(conclusions)Tj
4.9436 0 Td
(and)Tj
1.7291 0 Td
(to)Tj
1.0262 0 Td
(prevent)Tj
3.2541 0 Td
(such)Tj
2.0636 0 Td
(genomes)Tj
3.7644 0 Td
(from)Tj
2.2054 0 Td
(polluting)Tj
3.8437 0 Td
(the)Tj
1.474 0 Td
(reference)Tj
3.9175 0 Td
(databases,)Tj
-33.4259 -1.2983 Td
(which)Tj
2.6475 0 Td
(would)Tj
2.7156 0 Td
(lead)Tj
1.8481 0 Td
(to)Tj
1.0262 0 Td
(misclassifying)Tj
5.7826 0 Td
(newly)Tj
2.5795 0 Td
(obtained)Tj
3.7304 0 Td
(\(e.g.,)Tj
2.126 0 Td
(metagenomic\))Tj
5.9924 0 Td
(sequences.)Tj
-27.2521 -1.3039 Td
(Recognizing)Tj
5.1703 0 Td
(contaminant)Tj
5.3518 0 Td
(sequences)Tj
4.2179 0 Td
(in)Tj
1.0375 0 Td
(genome)Tj
3.4072 0 Td
(assemblies,)Tj
4.6488 0 Td
(whether)Tj
3.4753 0 Td
(prior)Tj
2.2507 0 Td
(or)Tj
1.0998 0 Td
(after)Tj
2.0353 0 Td
(public)Tj
-33.8908 -1.2983 Td
(release,)Tj
3.1294 0 Td
(is)Tj
0.8447 0 Td
(not)Tj
1.5761 0 Td
(a)Tj
0.6519 0 Td
(trivial)Tj
2.5568 0 Td
(task.)Tj
2.0353 0 Td
(When)Tj
2.6872 0 Td
(such)Tj
2.058 0 Td
(foreign)Tj
3.0954 0 Td
(sequences)Tj
4.2179 0 Td
(originate)Tj
3.7984 0 Td
(from)Tj
2.211 0 Td
(expected)Tj
3.7191 0 Td
(sources)Tj
-32.5812 -1.2983 Td
(\(e.g.,)Tj
2.1259 0 Td
(bacterial)Tj
3.6227 0 Td
(cloning)Tj
3.2258 0 Td
(vectors,)Tj
3.2825 0 Td
(human)Tj
3.0784 0 Td
(contamination\),)Tj
6.6897 0 Td
(they)Tj
1.9219 0 Td
(are)Tj
1.4513 0 Td
(easy)Tj
1.8935 0 Td
(to)Tj
1.0262 0 Td
(detect)Tj
2.6135 0 Td
(and)Tj
1.7291 0 Td
(remove,)Tj
3.4469 0 Td
(for)Tj
-36.1074 -1.2982 Td
(example)Tj
3.5489 0 Td
(by)Tj
1.1792 0 Td
(mapping)Tj
3.7927 0 Td
(raw)Tj
1.7065 0 Td
(sequencing)Tj
4.7168 0 Td
(reads)Tj
2.3357 0 Td
(against)Tj
3.0274 0 Td
(complete)Tj
3.8835 0 Td
(reference)Tj
3.9118 0 Td
(genomes)Tj
3.77 0 Td
(of)Tj
1.0148 0 Td
(usual)Tj
2.3187 0 Td
(con-)Tj
-35.206 -1.3039 Td
(taminant)Tj
3.855 0 Td
(organisms,)Tj
4.5695 0 Td
(as)Tj
1.0091 0 Td
(part)Tj
1.8312 0 Td
(of)Tj
1.0034 0 Td
(read)Tj
1.9673 0 Td
(quality)Tj
2.9423 0 Td
(control)Tj
3.1124 0 Td
(before)Tj
2.7326 0 Td
(genome)Tj
3.3959 0 Td
(assembly)Tj
3.8154 0 Td
(\(e.g.,)Tj
2.1146 0 Td
(BBsplit)Tj
3.0614 0 Td
(avail-)Tj
-35.4101 -1.2983 Td
(able)Tj
1.8311 0 Td
(at)Tj
0.83 0.64 0.02 0 k
0.9525 0 Td
(https://sourceforge.net/projects)Tj
12.5403 0 Td
(/bbmap/)Tj
0 g
(\).)Tj
4.2293 0 Td
(A)Tj
0.9014 0 Td
(complication)Tj
5.4822 0 Td
(arises)Tj
2.4378 0 Td
(with)Tj
1.9956 0 Td
(contamination)Tj
-30.3702 -1.2983 Td
(sources)Tj
3.1917 0 Td
(closely)Tj
2.8857 0 Td
(related)Tj
2.9423 0 Td
(to)Tj
1.0262 0 Td
(the)Tj
1.4683 0 Td
(organism\(s\))Tj
5.0343 0 Td
(of)Tj
1.0148 0 Td
(interest)Tj
3.2145 0 Td
(\(e.g.,)Tj
2.1259 0 Td
(human)Tj
3.0728 0 Td
(diversity)Tj
3.6453 0 Td
(studies)Tj
2.9877 0 Td
(or)Tj
1.0998 0 Td
(ancient)Tj
-33.7093 -1.3039 Td
(DNA)Tj
2.3754 0 Td
(studies\).)Tj
3.5489 0 Td
(These)Tj
2.5682 0 Td
(often)Tj
2.2847 0 Td
(require)Tj
3.1124 0 Td
(special)Tj
2.8913 0 Td
(precautions,)Tj
5.1251 0 Td
(both)Tj
2.0636 0 Td
(in)Tj
1.0318 0 Td
(the)Tj
1.474 0 Td
(laboratory)Tj
4.3483 0 Td
(and)Tj
1.7291 0 Td
(in)Tj
1.0375 0 Td
(down-)Tj
-33.5903 -1.2982 Td
(stream)Tj
2.9253 0 Td
(analyses)Tj
3.4866 0 Td
([)Tj
0.83 0.64 0.02 0 k
(18)Tj
0 g
(].)Tj
2.0749 0 Td
(Similarly,)Tj
4.0252 0 Td
(parallel)Tj
3.1408 0 Td
(processing)Tj
4.4673 0 Td
(of)Tj
1.0148 0 Td
(multiple)Tj
3.566 0 Td
(organisms,)Tj
4.5751 0 Td
(evolutionary)Tj
5.2611 0 Td
(related)Tj
-34.5371 -1.2983 Td
(or)Tj
1.0941 0 Td
(not,)Tj
1.8028 0 Td
(is)Tj
0.8448 0 Td
(expected)Tj
3.7247 0 Td
(to)Tj
1.0261 0 Td
(result)Tj
2.4491 0 Td
(in)Tj
1.0318 0 Td
(cross-contamination)Tj
8.4982 0 Td
(events.)Tj
2.9537 0 Td
(Yet,)Tj
1.8028 0 Td
(in)Tj
1.0318 0 Td
(this)Tj
1.6781 0 Td
(case,)Tj
2.0863 0 Td
(new)Tj
1.8766 0 Td
(sequences)Tj
4.2179 0 Td
(can)Tj
-36.1188 -1.3039 Td
(be)Tj
1.1508 0 Td
(attributed)Tj
4.1726 0 Td
(to)Tj
1.0261 0 Td
(their)Tj
2.109 0 Td
(true)Tj
1.8368 0 Td
(source)Tj
2.8346 0 Td
(based)Tj
2.4718 0 Td
(on)Tj
1.2756 0 Td
(the)Tj
1.474 0 Td
(comparison)Tj
4.972 0 Td
(of)Tj
1.0148 0 Td
(their)Tj
2.1089 0 Td
(sequencing)Tj
4.7168 0 Td
(coverage)Tj
3.7247 0 Td
(across)Tj
-34.8885 -1.2983 Td
(the)Tj
1.4683 0 Td
(different)Tj
3.6567 0 Td
(samples)Tj
3.3845 0 Td
(\(Simion)Tj
3.4412 0 Td
(et)Tj
0.9411 0 Td
(al.,)Tj
1.355 0 Td
(2018,)Tj
2.3471 0 Td
(in)Tj
1.4286 0 Td
(press\).)Tj
3.2088 0 Td
(With)Tj
2.2791 0 Td
(organisms)Tj
4.3539 0 Td
(belonging)Tj
4.201 0 Td
(to)Tj
1.0261 0 Td
(taxonomic)Tj
-33.0914 -1.2983 Td
(groups)Tj
2.9706 0 Td
(for)Tj
1.3833 0 Td
(which)Tj
2.6532 0 Td
(\(high-quality\))Tj
5.7714 0 Td
(representative)Tj
5.8336 0 Td
(genomes)Tj
3.7701 0 Td
(are)Tj
1.4513 0 Td
(already)Tj
3.1068 0 Td
(available,)Tj
3.8947 0 Td
(identifying)Tj
4.5751 0 Td
(the)Tj
-35.4101 -1.3039 Td
(genuinely)Tj
4.1215 0 Td
(homologous)Tj
5.1987 0 Td
(sequences)Tj
4.2179 0 Td
(is)Tj
0.8504 0 Td
(easy.)Tj
2.1147 0 Td
(In)Tj
1.1111 0 Td
(contrast,)Tj
3.685 0 Td
(sequences)Tj
4.218 0 Td
(for)Tj
1.3889 0 Td
(which)Tj
2.6476 0 Td
(there)Tj
2.2677 0 Td
(exists)Tj
2.3924 0 Td
(no)Tj
1.2756 0 Td
(close)Tj
-35.4895 -1.2982 Td
(counterpart)Tj
4.9379 0 Td
(in)Tj
1.0374 0 Td
(the)Tj
1.4684 0 Td
(corresponding)Tj
6.0604 0 Td
(reference)Tj
3.9175 0 Td
(genomes)Tj
3.77 0 Td
(can)Tj
1.6214 0 Td
(be)Tj
1.1509 0 Td
(anything)Tj
3.7644 0 Td
(from)Tj
2.2053 0 Td
(divergent)Tj
4.0025 0 Td
(paralo-)Tj
-33.9361 -1.2983 Td
(gues)Tj
1.9955 0 Td
(to)Tj
1.0262 0 Td
(new)Tj
1.8765 0 Td
(genes,)Tj
2.6645 0 Td
(possibly)Tj
3.4413 0 Td
(acquired)Tj
3.702 0 Td
(horizontally,)Tj
5.2667 0 Td
(or)Tj
1.0999 0 Td
(even)Tj
2.0693 0 Td
(foreign)Tj
3.0897 0 Td
(regions)Tj
3.1634 0 Td
(from)Tj
2.2054 0 Td
(co-sequenced)Tj
-31.6004 -1.2983 Td
(organisms.)Tj
4.5807 0 Td
(Finally,)Tj
3.1691 0 Td
(when)Tj
2.4038 0 Td
(both)Tj
2.0579 0 Td
(the)Tj
1.4684 0 Td
(genome)Tj
3.4072 0 Td
(under)Tj
2.6192 0 Td
(study)Tj
2.3924 0 Td
(and)Tj
1.7291 0 Td
(its)Tj
1.1452 0 Td
(potential)Tj
3.7644 0 Td
(contaminants)Tj
5.7089 0 Td
(belong)Tj
-34.4463 -1.3039 Td
(to)Tj
1.0261 0 Td
(new)Tj
1.8765 0 Td
(or)Tj
1.0942 0 Td
(scarcely)Tj
3.3618 0 Td
(sampled)Tj
3.549 0 Td
(groups,)Tj
3.1918 0 Td
(as)Tj
1.0148 0 Td
(in)Tj
1.0375 0 Td
(the)Tj
1.4683 0 Td
(context)Tj
3.1861 0 Td
(of)Tj
1.0148 0 Td
(large-scale)Tj
4.3994 0 Td
(phylogenomic)Tj
5.9243 0 Td
(studies,)Tj
3.2145 0 Td
(sepa-)Tj
-35.3591 -1.2983 Td
(rating)Tj
2.6021 0 Td
(the)Tj
1.4684 0 Td
(wheat)Tj
2.5908 0 Td
(from)Tj
2.2054 0 Td
(the)Tj
1.4683 0 Td
(chaff)Tj
2.1827 0 Td
(can)Tj
1.627 0 Td
(become)Tj
3.3222 0 Td
(very)Tj
1.9219 0 Td
(challenging)Tj
4.8189 0 Td
([)Tj
0.83 0.64 0.02 0 k
(19)Tj
0 g
(].)Tj
-0.018 Tc
-23.0115 -1.2982 Td
(Cyanobacteria,)Tj
6.015 0 Td
(traditionally)Tj
4.9436 0 Td
(called)Tj
2.4321 0 Td
(blue-green)Tj
4.371 0 Td
(algae,)Tj
2.3641 0 Td
(form)Tj
2.1487 0 Td
(a)Tj
0.6406 0 Td
(large)Tj
2.0919 0 Td
(and)Tj
1.6838 0 Td
(morphologically)Tj
6.5537 0 Td
(diverse)Tj
-34.4407 -1.3039 Td
(group)Tj
2.5398 0 Td
(of)Tj
0.9864 0 Td
(bacteria)Tj
3.2655 0 Td
([)Tj
0.83 0.64 0.02 0 k
(13)Tj
0 g
(],)Tj
2.0069 0 Td
(which)Tj
2.5795 0 Td
(are)Tj
1.406 0 Td
(of)Tj
0.9865 0 Td
(primary)Tj
3.3562 0 Td
(interest)Tj
3.1011 0 Td
(in)Tj
1.0091 0 Td
(ecological,)Tj
4.2349 0 Td
(palaeobiogeology)Tj
6.9052 0 Td
(and)Tj
1.6894 0 Td
(evolu-)Tj
-34.0665 -1.2983 Td
(tionary)Tj
2.999 0 Td
(studies.)Tj
3.1011 0 Td
(Hence,)Tj
2.948 0 Td
(the)Tj
1.4286 0 Td
(appearance)Tj
4.6091 0 Td
(of)Tj
0.9865 0 Td
(oxygenic)Tj
3.6623 0 Td
(photosynthesis)Tj
5.9811 0 Td
(in)Tj
1.0091 0 Td
(this)Tj
1.6158 0 Td
(phylum)Tj
3.2314 0 Td
(had)Tj
1.6668 0 Td
(a)Tj
0.6406 0 Td
(critical)Tj
-33.8794 -1.2983 Td
(impact)Tj
2.8969 0 Td
(on)Tj
1.2473 0 Td
(early)Tj
2.0749 0 Td
(Earth,)Tj
2.5625 0 Td
(its)Tj
1.1055 0 Td
(evolution,)Tj
4.0876 0 Td
(and)Tj
1.6894 0 Td
(on)Tj
1.2472 0 Td
(the)Tj
1.4287 0 Td
(early)Tj
2.0749 0 Td
(biosphere)Tj
4.0025 0 Td
(by)Tj
1.1509 0 Td
(increasing)Tj
4.1896 0 Td
(the)Tj
1.4286 0 Td
(level)Tj
1.9446 0 Td
(of)Tj
0.9864 0 Td
(free)Tj
1.6725 0 Td
(oxy-)Tj
-35.79 -1.3039 Td
(gen)Tj
1.6157 0 Td
(in)Tj
1.0034 0 Td
(the)Tj
1.4287 0 Td
(ocean)Tj
2.4888 0 Td
(and)Tj
1.6894 0 Td
(atmosphere,)Tj
4.972 0 Td
(creating)Tj
3.3392 0 Td
(new)Tj
1.8368 0 Td
(ecological)Tj
4.0195 0 Td
(niches)Tj
2.6872 0 Td
([)Tj
0.83 0.64 0.02 0 k
(20)Tj
0 g
()Tj
0.83 0.64 0.02 0 k
(22)Tj
0 g
(].)Tj
3.4356 0 Td
(Today,)Tj
2.897 0 Td
(they)Tj
1.8652 0 Td
(colonize)Tj
3.4469 0 Td
(a)Tj
-36.7254 -1.2982 Td
(wide)Tj
2.0636 0 Td
(range)Tj
2.3924 0 Td
(of)Tj
0.9864 0 Td
(illuminated)Tj
4.6715 0 Td
(ecosystems,)Tj
4.7282 0 Td
(from)Tj
2.1486 0 Td
(human-managed)Tj
6.8995 0 Td
(to)Tj
0.9978 0 Td
(extremophile,)Tj
5.5502 0 Td
(and)Tj
1.6894 0 Td
(from)Tj
2.1487 0 Td
(marine)Tj
ET
Q
q
1 j
1 J
0 w
576 737.1 m
36 737.1 l
36 737.6 l
576 737.6 l
f*
36 741.2598 107.1496 23.6976 re
W* n
q
107.0929 0 0 23.6409 36 741.3165 cm
q
/I0 Do
Q
Q
Q
q
0 0 612 792 re
W* n
1 j
1 J
0 w
7.9999 0 0 7.9999 412.6677 745.7952 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(Contam)Tj
3.4441 0 Td
(ination)Tj
3.1039 0 Td
(level)Tj
2.2323 0 Td
(of)Tj
1.0418 0 Td
(cyanobac)Tj
4.2024 0 Td
(terial)Tj
2.3386 0 Td
(genomes)Tj
ET
Q
q
1 j
1 J
0 w
36 48.0002 m
576 48.0002 l
576 47.5002 l
36 47.5002 l
f*
0.83 0.64 0.02 0 k
81.5811 34.9228 m
237.8835 34.9228 l
h
f*
0 g
7.9999 0 0 7.9999 36 36 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(PLOS)Tj
2.8559 0 Td
(ONE)Tj
2.3669 0 Td
(|)Tj
0.83 0.64 0.02 0 k
0.4748 0 Td
(https://doi.or)Tj
5.4142 0 Td
(g/10.137)Tj
3.8198 0 Td
(1/journal.po)Tj
5.1236 0 Td
(ne.02003)Tj
4.089 0 Td
(23)Tj
0 g
2.0906 0 Td
(July)Tj
1.9701 0 Td
(25,)Tj
1.5874 0 Td
(2018)Tj
35.3483 0 Td
(2)Tj
0.7654 0 Td
(/)Tj
0.496 0 Td
(26)Tj
/F9 1 Tf
-0.025 Tc
-66.402 84.0904 Td
(\(AW\),)Tj
2.3882 0 Td
(the)Tj
1.3748 0 Td
(BELSPO)Tj
3.3307 0 Td
(Interunive)Tj
3.6922 0 Td
(rsity)Tj
1.8212 0 Td
(Attracti)Tj
2.6292 0 Td
(on)Tj
1.1693 0 Td
(Pole)Tj
-16.4056 -1.3748 Td
(Planet)Tj
2.5086 0 Td
(TOPERS)Tj
3.3945 0 Td
(\(EJJ)Tj
1.8426 0 Td
(and)Tj
1.5874 0 Td
(LC\),)Tj
1.7504 0 Td
(and)Tj
1.5874 0 Td
(the)Tj
1.3748 0 Td
(TULIP)Tj
-14.0457 -1.3749 Td
(Laboratory)Tj
4.2449 0 Td
(of)Tj
0.9496 0 Td
(Excellence)Tj
4.0819 0 Td
(\(ANR-10-LAB)Tj
5.0953 0 Td
(X-41\))Tj
2.3103 0 Td
(\(HP\).)Tj
-16.682 -1.3748 Td
(LC,)Tj
1.4456 0 Td
(LM,)Tj
1.6654 0 Td
(MVV,)Tj
2.2536 0 Td
(RRL)Tj
1.8638 0 Td
(and)Tj
1.5945 0 Td
(BD)Tj
1.3322 0 Td
(are)Tj
1.3678 0 Td
(all)Tj
1.0275 0 Td
(FRIA)Tj
2.0127 0 Td
(\(Fonds)Tj
-14.5631 -1.3748 Td
(pour)Tj
1.9488 0 Td
(la)Tj
0.8362 0 Td
(formation)Tj
/F10 1 Tf
3.8268 0 Td
[( j)]TJ
/F9 1 Tf
0.6378 0 Td
(la)Tj
0.8362 0 Td
(Recherche)Tj
4.167 0 Td
(dans)Tj
2.0126 0 Td
(l'Industr)Tj
3.0402 0 Td
(ie)Tj
0.8362 0 Td
(et)Tj
-18.1418 -1.3748 Td
(l'Agricultu)Tj
3.6992 0 Td
(re\))Tj
1.2614 0 Td
(fellows)Tj
2.8134 0 Td
(of)Tj
0.9496 0 Td
(the)Tj
1.3678 0 Td
(FRS-FNRS.)Tj
4.4079 0 Td
(AW)Tj
1.552 0 Td
(is)Tj
0.8362 0 Td
(a)Tj
-16.8875 -1.3748 Td
(Research)Tj
3.6992 0 Td
(Associate)Tj
3.7701 0 Td
(of)Tj
0.9496 0 Td
(the)Tj
1.3677 0 Td
(FRS-FNRS.)Tj
4.4079 0 Td
(AM's)Tj
2.119 0 Td
(stay)Tj
1.7362 0 Td
(in)Tj
-18.0497 -1.3748 Td
(University)Tj
3.9189 0 Td
(of)Tj
0.9425 0 Td
(Li)Tj
/F10 1 Tf
[( q)]TJ
/F9 1 Tf
(ge)Tj
2.204 0 Td
(was)Tj
1.7008 0 Td
(partially)Tj
3.1039 0 Td
(financed)Tj
3.352 0 Td
(by)Tj
1.1126 0 Td
(a)Tj
-16.3347 -1.3748 Td
(bilateral)Tj
3.0968 0 Td
(cooperation)Tj
4.6134 0 Td
([ARTHRO)Tj
3.6497 0 Td
(-ARN:)Tj
2.452 0 Td
(Functional)Tj
-13.8119 -1.3748 Td
(genomics)Tj
3.6283 0 Td
(-based)Tj
2.7426 0 Td
(approach)Tj
3.685 0 Td
(for)Tj
1.2544 0 Td
(the)Tj
1.3748 0 Td
(design)Tj
2.6717 0 Td
(of)Tj
0.9496 0 Td
(genetic)Tj
-16.3064 -1.3749 Td
(engineerin)Tj
3.848 0 Td
(g)Tj
0.6945 0 Td
(tools)Tj
2.041 0 Td
(in)Tj
0.8858 0 Td
(the)Tj
1.3677 0 Td
(edible)Tj
2.3953 0 Td
(cyanobacteri)Tj
4.7056 0 Td
(um)Tj
-15.9379 -1.3748 Td
(Arthrospir)Tj
3.7346 0 Td
(a.)Tj
0.8717 0 Td
(Scientifi)Tj
2.9268 0 Td
(c)Tj
0.6449 0 Td
(and)Tj
1.5874 0 Td
(technical)Tj
3.4937 0 Td
(cooperati)Tj
3.437 0 Td
(on)Tj
-16.6961 -1.3748 Td
(between)Tj
3.3236 0 Td
(Republic)Tj
3.4583 0 Td
(of)Tj
0.9496 0 Td
(Poland)Tj
2.778 0 Td
(and)Tj
1.5874 0 Td
(Belgium)Tj
-12.0969 -1.3748 Td
(\(Fe)Tj
0 Tc
0.7937 0.0283 Td
()Tj
-0.025 Tc
0.3543 -0.0283 Td
(de)Tj
0 Tc
0.5386 0.0283 Td
()Tj
-0.025 Tc
0.3614 -0.0283 Td
(ration)Tj
2.3386 0 Td
(Wallonie-Brux)Tj
5.2087 0 Td
(elles\))Tj
2.1827 0 Td
(\(2014-2)Tj
2.9764 0 Td
(016\)].)Tj
-14.7544 -1.3748 Td
(Computat)Tj
3.6283 0 Td
(ional)Tj
1.9772 0 Td
(resources)Tj
3.8906 0 Td
(were)Tj
2.0055 0 Td
(provided)Tj
3.4583 0 Td
(by)Tj
1.1197 0 Td
(the)Tj
-16.0796 -1.3748 Td
(Consortiu)Tj
3.5929 0 Td
(m)Tj
0.978 0 Td
(des)Tj
1.5378 0 Td
(E)Tj
0 Tc
0.0779 0.2126 Td
()Tj
-0.025 Tc
0.3898 -0.2126 Td
(quipements)Tj
4.5851 0 Td
(de)Tj
1.1126 0 Td
(Calcul)Tj
2.452 0 Td
(Intensi)Tj
2.4874 0 Td
(f)Tj
-17.2135 -1.3748 Td
(\(CE)Tj
0 Tc
0.9141 0.2126 Td
()Tj
-0.025 Tc
0.3898 -0.2126 Td
(CI\),)Tj
1.5307 0 Td
(funded)Tj
2.7922 0 Td
(by)Tj
1.1197 0 Td
(the)Tj
1.3677 0 Td
(F.R.S.-FNR)Tj
4.1103 0 Td
(S)Tj
0.7441 0 Td
(\(2.5020.11)Tj
4.0677 0 Td
(\),)Tj
-17.0363 -1.3749 Td
(and)Tj
1.5874 0 Td
(through)Tj
3.1535 0 Td
(two)Tj
1.5874 0 Td
(grants)Tj
2.5725 0 Td
(to)Tj
0.9496 0 Td
(DB)Tj
1.3323 0 Td
(\(Universit)Tj
3.5788 0 Td
(y)Tj
0.6449 0 Td
(of)Tj
0.9425 0 Td
(Li)Tj
/F10 1 Tf
[( q)]TJ
/F9 1 Tf
(ge)Tj
-16.3489 -1.3819 Td
(Cre)Tj
0 Tc
1.2543 0.0355 Td
()Tj
-0.025 Tc
0.3614 -0.0355 Td
(dit)Tj
1.141 0 Td
(de)Tj
1.1126 0 Td
(de)Tj
0 Tc
0.5386 0.0355 Td
()Tj
-0.025 Tc
0.3543 -0.0355 Td
(marrage)Tj
3.3307 0 Td
(2012)Tj
2.4733 0 Td
(SFRD-12/)Tj
3.6283 0 Td
(04;)Tj
1.389 0 Td
(F.R.S.-)Tj
-15.5835 -1.3748 Td
(FNRS)Tj
2.3386 0 Td
(Cre)Tj
0 Tc
1.2543 0.0355 Td
()Tj
-0.025 Tc
0.3614 -0.0355 Td
(dit)Tj
1.141 0 Td
(de)Tj
1.1197 0 Td
(recherche)Tj
3.8835 0 Td
(2014)Tj
2.4732 0 Td
(CDR)Tj
1.9205 0 Td
(J.0080.15\).)Tj
/F8 1 Tf
-14.4922 -2.1189 Td
(Competing)Tj
4.3795 0 Td
(interests)Tj
3.3307 0 Td
(:)Tj
/F9 1 Tf
0.4819 0 Td
(The)Tj
1.5875 0 Td
(authors)Tj
3.0401 0 Td
(have)Tj
1.963 0 Td
(declared)Tj
-14.7827 -1.3748 Td
(that)Tj
1.6228 0 Td
(no)Tj
1.1693 0 Td
(competing)Tj
4.1599 0 Td
(interests)Tj
ET
endstream
endobj
46 0 obj
<>stream
endstream
endobj
47 0 obj
<>stream
endstream
endobj
48 0 obj
<>stream
endstream
endobj
49 0 obj
<>stream
endstream
endobj
50 0 obj
<>stream
endstream
endobj
51 0 obj
<>stream
endstream
endobj
52 0 obj
<>stream
endstream
endobj
53 0 obj
<>stream
endstream
endobj
54 0 obj
<>stream
endstream
endobj
55 0 obj
<>stream
endstream
endobj
56 0 obj
<>stream
endstream
endobj
57 0 obj
<>stream
endstream
endobj
58 0 obj
<>stream
endstream
endobj
59 0 obj
<>stream
endstream
endobj
60 0 obj
<>stream
endstream
endobj
61 0 obj
<>stream
endstream
endobj
62 0 obj
<>stream
endstream
endobj
63 0 obj
<>stream
endstream
endobj
64 0 obj
<>stream
endstream
endobj
65 0 obj
<>stream
endstream
endobj
66 0 obj
<>stream
BT
10.3394 54.4681 Td
(exist.)Tj
ET
Q
endstream
endobj
67 0 obj
<>/XObject<>>>/CropBox[0 0 612 792]/MediaBox[0 0 612 792]/Parent 11 0 R/Annots 71 0 R/Contents 72 0 R/TrimBox[0 0 612 792]>>
endobj
71 0 obj
[73 0 R 74 0 R 75 0 R 76 0 R 77 0 R 78 0 R 79 0 R 80 0 R 81 0 R 82 0 R 83 0 R 84 0 R 85 0 R 86 0 R 87 0 R 88 0 R 89 0 R 90 0 R 91 0 R]
endobj
73 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref023)>>
endobj
74 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref006)>>
endobj
75 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref010)>>
endobj
76 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref006)>>
endobj
77 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref008)>>
endobj
78 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref024)>>
endobj
79 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref027)>>
endobj
80 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref028)>>
endobj
81 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref029)>>
endobj
82 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref028)>>
endobj
83 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref030)>>
endobj
84 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref031)>>
endobj
85 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.g001)>>
endobj
86 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref032)>>
endobj
87 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref033)>>
endobj
88 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref014)>>
endobj
89 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref034)>>
endobj
90 0 obj
<>/Border[0 0 0]/Dest(Rpone.0200323.ref035)>>
endobj
91 0 obj
<>/Border[0 0 0]/A 92 0 R>>
endobj
92 0 obj
<>
endobj
72 0 obj
[93 0 R 94 0 R 95 0 R 96 0 R 97 0 R 98 0 R 99 0 R 100 0 R 101 0 R 102 0 R 103 0 R 104 0 R 105 0 R 106 0 R 107 0 R 108 0 R 109 0 R 110 0 R 111 0 R]
endobj
93 0 obj
<>stream
q
0.83 0.64 0.02 0 k
527.4709 693.2976 m
536.7118 693.2976 l
h
f*
289.6441 667.3323 m
294.2929 667.3323 l
h
f*
296.3906 667.3323 m
305.6315 667.3323 l
h
f*
447.3638 667.3323 m
451.9559 667.3323 l
h
f*
454.1102 667.3323 m
458.7024 667.3323 l
h
f*
374.5701 628.3276 m
383.7543 628.3276 l
h
f*
388.8 628.3276 m
398.0409 628.3276 l
h
f*
299.7921 602.3055 m
309.0331 602.3055 l
h
f*
311.1307 602.3055 m
320.3717 602.3055 l
h
f*
215.7732 576.3402 m
225.0142 576.3402 l
h
f*
227.1118 576.3402 m
236.3528 576.3402 l
h
f*
238.4504 576.3402 m
247.6913 576.3402 l
h
f*
548.2205 302.9102 m
567.7228 302.9102 l
h
f*
276.0378 211.9181 m
285.5055 211.9181 l
h
f*
287.7732 211.9181 m
297.2976 211.9181 l
h
f*
352.5732 172.9134 m
362.0409 172.9134 l
h
f*
540.737 120.926 m
550.2614 120.926 l
h
f*
513.5244 94.9039 m
523.0488 94.9039 l
h
f*
0 g
1 j
1 J
0 w
10 0 0 10 200.0125 707.4141 cm
BT
/F7 1 Tf
1 TL
-0.018 Tc
0 0 Td
(or)Tj
1.0714 0 Td
(freshwater)Tj
4.2577 0 Td
(habitats)Tj
3.2371 0 Td
(\(as)Tj
1.3153 0 Td
(picoplankton)Tj
5.3631 0 Td
(or)Tj
1.0715 0 Td
(benthic)Tj
3.1124 0 Td
(mats\))Tj
2.4038 0 Td
(to)Tj
0.9977 0 Td
(hypersaline)Tj
4.6432 0 Td
(environments)Tj
5.6239 0 Td
(or)Tj
1.0715 0 Td
(hot)Tj
-34.1686 -1.3039 Td
(springs,)Tj
3.2258 0 Td
(in)Tj
1.0034 0 Td
(polar,)Tj
2.4378 0 Td
(temperate)Tj
4.1045 0 Td
(and)Tj
1.6895 0 Td
(tropical)Tj
3.1691 0 Td
(regions,)Tj
3.2768 0 Td
(with)Tj
1.9446 0 Td
(the)Tj
1.4286 0 Td
(exception)Tj
3.9685 0 Td
(of)Tj
0.9865 0 Td
(acidic)Tj
2.4774 0 Td
(waters)Tj
2.7099 0 Td
([)Tj
0.83 0.64 0.02 0 k
(23)Tj
0 g
(].)Tj
2.0069 0 Td
(Usually,)Tj
-34.4293 -1.2982 Td
(contaminants)Tj
5.5388 0 Td
(are)Tj
1.406 0 Td
(organisms)Tj
4.2293 0 Td
(that)Tj
1.7177 0 Td
(live)Tj
1.5534 0 Td
(in)Tj
1.0091 0 Td
(close)Tj
2.109 0 Td
(proximity)Tj
4.0592 0 Td
(to)Tj
0.9978 0 Td
(the)Tj
1.4286 0 Td
(sequenced)Tj
4.2576 0 Td
(organism)Tj
3.8778 0 Td
(\(i.e.,)Tj
1.8425 0 Td
(parasites,)Tj
-34.0268 -1.2983 Td
(symbionts,)Tj
4.4276 0 Td
(epiphytes\))Tj
4.2123 0 Td
([)Tj
0.83 0.64 0.02 0 k
(6)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(10)Tj
0 g
(])Tj
2.4661 0 Td
(or)Tj
1.0715 0 Td
(that)Tj
1.7235 0 Td
(are)Tj
1.4059 0 Td
(simultaneously)Tj
6.0435 0 Td
(studied)Tj
3.0557 0 Td
([)Tj
0.83 0.64 0.02 0 k
(6)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(8)Tj
0 g
(].)Tj
2.2223 0 Td
(It)Tj
0.8278 0 Td
(is)Tj
0.822 0 Td
(for)Tj
1.3436 0 Td
(instance)Tj
3.4129 0 Td
(well)Tj
1.7631 0 Td
(known)Tj
-34.7978 -1.2983 Td
(that)Tj
1.7234 0 Td
(growth)Tj
2.9877 0 Td
(of)Tj
0.9865 0 Td
(picocyanobacteria)Tj
7.2226 0 Td
(\()Tj
/F11 1 Tf
[()26()-13()6()7()13()6()4()7()4()7()1()-4( )]TJ
/F7 1 Tf
5.9527 0 Td
(and)Tj
/F11 1 Tf
1.6894 0 Td
[(\n)2()20()4()13()10()4()11()20()4()7()4()7()1()-4( )]TJ
/F7 1 Tf
(\))Tj
6.5537 0 Td
(is)Tj
0.8164 0 Td
(improved)Tj
3.9968 0 Td
(by)Tj
1.1565 0 Td
(mutualistic)Tj
-33.0857 -1.3039 Td
(interactions)Tj
4.7961 0 Td
(with)Tj
1.9446 0 Td
(heterotrophic)Tj
5.4992 0 Td
(organisms,)Tj
4.4447 0 Td
(which)Tj
2.5795 0 Td
(notably)Tj
3.1181 0 Td
(remove)Tj
3.1351 0 Td
(toxic)Tj
2.1089 0 Td
(reactive)Tj
3.2032 0 Td
(oxygen)Tj
2.999 0 Td
(species)Tj
-33.8284 -1.2982 Td
(from)Tj
2.1486 0 Td
(these)Tj
2.1827 0 Td
(phototroph/heterotroph)Tj
9.5923 0 Td
(systems)Tj
3.2032 0 Td
([)Tj
0.83 0.64 0.02 0 k
(24)Tj
0 g
()Tj
0.83 0.64 0.02 0 k
(27)Tj
0 g
(].)Tj
3.4355 0 Td
(Cyanobacteria)Tj
5.7997 0 Td
(are)Tj
1.4116 0 Td
(also)Tj
1.7121 0 Td
(known)Tj
2.9311 0 Td
(to)Tj
0.9977 0 Td
(excrete)Tj
-33.4145 -1.2983 Td
(different)Tj
3.5262 0 Td
(compounds,)Tj
5.0457 0 Td
(including)Tj
3.9174 0 Td
(polysaccharides,)Tj
6.5027 0 Td
(proteins,)Tj
3.6113 0 Td
(nucleic)Tj
2.982 0 Td
(acids,)Tj
2.3754 0 Td
(osmolytes,)Tj
4.2803 0 Td
(in)Tj
1.0091 0 Td
(their)Tj
-33.2501 -1.3039 Td
(immediate)Tj
4.3709 0 Td
(environment)Tj
5.2781 0 Td
([)Tj
0.83 0.64 0.02 0 k
(28)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(29)Tj
0 g
(].)Tj
3.1408 0 Td
(Bacteria)Tj
3.3392 0 Td
(from)Tj
2.1543 0 Td
(other)Tj
2.2734 0 Td
(phyla,)Tj
2.5455 0 Td
(such)Tj
2.0012 0 Td
(as)Tj
0.9865 0 Td
(Bacteroidetes)Tj
5.3801 0 Td
(and)Tj
1.6838 0 Td
(Proteobac-)Tj
-33.1538 -1.2983 Td
(teria,)Tj
2.1543 0 Td
(feed)Tj
1.8255 0 Td
(on)Tj
1.2472 0 Td
(those)Tj
2.2677 0 Td
(extracellular)Tj
4.9493 0 Td
(productions)Tj
4.9209 0 Td
(and)Tj
1.6894 0 Td
(thus)Tj
1.8822 0 Td
(live)Tj
1.5534 0 Td
(in)Tj
1.0091 0 Td
(close)Tj
2.109 0 Td
(relationship)Tj
4.8245 0 Td
(with)Tj
1.9389 0 Td
(Cyanobacte-)Tj
-32.3714 -1.2983 Td
(ria)Tj
1.2472 0 Td
([)Tj
0.83 0.64 0.02 0 k
(28)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(30)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(31)Tj
0 g
(].)Tj
4.2803 0 Td
(Because)Tj
3.2938 0 Td
(of)Tj
0.9865 0 Td
(this)Tj
1.6157 0 Td
(trophic)Tj
3.0331 0 Td
(coupling,)Tj
3.8267 0 Td
(the)Tj
1.423 0 Td
(majority)Tj
3.5206 0 Td
(of)Tj
0.9864 0 Td
(available)Tj
3.5377 0 Td
(cyanobacterial)Tj
5.7996 0 Td
(strains)Tj
2.7609 0 Td
(are)Tj
-36.3115 -1.3039 Td
(not)Tj
1.5306 0 Td
(axenic,)Tj
2.9084 0 Td
(hence)Tj
2.5001 0 Td
(resulting)Tj
3.6 0 Td
(in)Tj
1.0091 0 Td
(potential)Tj
3.634 0 Td
(genome)Tj
3.3222 0 Td
(contamination.)Tj
6.1511 0 Td
(In)Tj
1.0829 0 Td
(this)Tj
1.6157 0 Td
(respect,)Tj
3.1521 0 Td
(we)Tj
1.2983 0 Td
(recently)Tj
-31.8045 -1.2982 Td
(noticed)Tj
3.118 0 Td
(that)Tj
1.7235 0 Td
(six)Tj
1.2699 0 Td
(genome)Tj
3.3222 0 Td
(assemblies)Tj
4.2859 0 Td
(\(GCA_000472885.1,)Tj
8.0844 0 Td
(GCA_000817745.1,)Tj
7.7612 0 Td
(GCA_000817775.1)Tj
7.336 0 Td
(,)Tj
-36.9011 -1.2983 Td
(GCA_000817785.1,)Tj
7.7612 0 Td
(GCA_000817735.1,)Tj
7.7612 0 Td
(GCA_000828075.1\))Tj
7.8802 0 Td
(presented)Tj
3.9855 0 Td
(two)Tj
1.6668 0 Td
(or)Tj
1.0715 0 Td
(even)Tj
2.0126 0 Td
(three)Tj
2.194 0 Td
(copies)Tj
-34.333 -1.3039 Td
(of)Tj
0.9864 0 Td
(many)Tj
2.4208 0 Td
(proteins)Tj
3.4015 0 Td
(usually)Tj
2.9197 0 Td
(encoded)Tj
3.5036 0 Td
(by)Tj
1.1509 0 Td
(a)Tj
0.6406 0 Td
(single)Tj
2.4491 0 Td
(gene,)Tj
2.2337 0 Td
(one)Tj
1.6611 0 Td
(being)Tj
2.3584 0 Td
(the)Tj
1.4286 0 Td
(likely)Tj
2.2677 0 Td
(genuine)Tj
3.3279 0 Td
(cyanobacterial)Tj
-30.75 -1.2983 Td
(protein)Tj
3.0557 0 Td
(and)Tj
1.6837 0 Td
(the)Tj
1.4287 0 Td
(other)Tj
2.279 0 Td
(one\(s\))Tj
2.6589 0 Td
(being)Tj
2.3584 0 Td
(closely)Tj
2.7836 0 Td
(related)Tj
2.846 0 Td
(to)Tj
0.9978 0 Td
(non-cyanobacterial)Tj
7.6932 0 Td
(species)Tj
2.9026 0 Td
(\(data)Tj
2.1827 0 Td
(not)Tj
1.5307 0 Td
(shown\).)Tj
-0.004 Tc
-33.2048 -1.2982 Td
(As)Tj
1.2699 0 Td
(these)Tj
2.2507 0 Td
(observations)Tj
5.261 0 Td
(prompted)Tj
4.201 0 Td
(us)Tj
1.1111 0 Td
(to)Tj
1.0262 0 Td
(investigate)Tj
4.4617 0 Td
(the)Tj
1.4683 0 Td
(issue)Tj
2.16 0 Td
(thoroughly,)Tj
4.8756 0 Td
(we)Tj
1.3322 0 Td
(designed)Tj
3.7587 0 Td
(a)Tj
0.6577 0 Td
(novel)Tj
-35.0303 -1.2983 Td
(strategy,)Tj
3.5489 0 Td
(based)Tj
2.4718 0 Td
(on)Tj
1.2756 0 Td
(state-of-the-art)Tj
6.2362 0 Td
(tools,)Tj
2.364 0 Td
(to)Tj
1.0262 0 Td
(evaluate)Tj
3.4639 0 Td
(the)Tj
1.4683 0 Td
(contamination)Tj
6.1228 0 Td
(level)Tj
2.0126 0 Td
(of)Tj
1.0148 0 Td
(publicly)Tj
3.4129 0 Td
(avail-)Tj
-34.418 -1.3039 Td
(able)Tj
1.8311 0 Td
(genomes.)Tj
3.9912 0 Td
(Altogether,)Tj
4.6941 0 Td
(our)Tj
1.6214 0 Td
(analyses)Tj
3.4866 0 Td
(allowed)Tj
3.2882 0 Td
(us)Tj
1.1055 0 Td
(to)Tj
1.0261 0 Td
(establish)Tj
3.6454 0 Td
(a)Tj
0.6576 0 Td
(global)Tj
2.6249 0 Td
(ranking)Tj
3.3505 0 Td
(of)Tj
1.0148 0 Td
(440)Tj
1.6441 0 Td
(cyano-)Tj
-33.9815 -1.2983 Td
(bacterial)Tj
3.6226 0 Td
(genome)Tj
3.4072 0 Td
(assemblies,)Tj
4.6488 0 Td
(from)Tj
2.2054 0 Td
(the)Tj
1.474 0 Td
(most)Tj
2.2053 0 Td
(contaminated)Tj
5.7486 0 Td
(to)Tj
1.0262 0 Td
(the)Tj
1.4683 0 Td
(least)Tj
1.9842 0 Td
(contaminated.)Tj
5.9754 0 Td
(These)Tj
-33.766 -1.2983 Td
(results)Tj
2.8062 0 Td
(suggest)Tj
3.1238 0 Td
(that)Tj
1.7801 0 Td
(genome)Tj
3.4073 0 Td
(producers)Tj
4.2462 0 Td
(should)Tj
2.9197 0 Td
(strive)Tj
2.3981 0 Td
(to)Tj
1.0205 0 Td
(upload)Tj
2.982 0 Td
(genomic)Tj
3.6737 0 Td
(sequences)Tj
4.2179 0 Td
(devoid)Tj
2.931 0 Td
(of)Tj
-35.5065 -1.3039 Td
(contamination)Tj
6.1227 0 Td
(and)Tj
1.7292 0 Td
(that)Tj
1.7744 0 Td
(genome)Tj
3.4073 0 Td
(consumers)Tj
4.5637 0 Td
(should)Tj
2.9197 0 Td
(be)Tj
1.1508 0 Td
(cautious)Tj
3.566 0 Td
(when)Tj
2.4038 0 Td
(analyzing)Tj
4.0308 0 Td
(such)Tj
2.058 0 Td
(data)Tj
1.9162 0 Td
(in)Tj
-35.6426 -1.2982 Td
(downstream)Tj
5.193 0 Td
(studies.)Tj
3.2145 0 Td
(Moreover,)Tj
4.3936 0 Td
(we)Tj
1.3266 0 Td
(advocate)Tj
3.7247 0 Td
(the)Tj
1.4684 0 Td
(stance)Tj
2.7099 0 Td
(that)Tj
1.7801 0 Td
(raw)Tj
1.7065 0 Td
(sequencing)Tj
4.7168 0 Td
(reads)Tj
2.3357 0 Td
(should)Tj
2.9197 0 Td
(be)Tj
-35.4895 -1.2983 Td
(released)Tj
3.4298 0 Td
(along)Tj
2.4208 0 Td
(with)Tj
1.9956 0 Td
(newly)Tj
2.5795 0 Td
(assembled)Tj
4.32 0 Td
(genomes,)Tj
3.9968 0 Td
(so)Tj
1.0885 0 Td
(as)Tj
1.0148 0 Td
(to)Tj
1.0261 0 Td
(help)Tj
1.9333 0 Td
(genome)Tj
3.4072 0 Td
(scientists)Tj
3.8267 0 Td
(to)Tj
1.0262 0 Td
(evaluate)Tj
3.4639 0 Td
(the)Tj
-35.5292 -1.3039 Td
(quality)Tj
2.9536 0 Td
(of)Tj
1.0148 0 Td
(primary)Tj
3.4583 0 Td
(data.)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 366.0094 cm
BT
/F2 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Results)Tj
3.7984 0 Td
(and)Tj
1.989 0 Td
(discussion)Tj
/F12 1 Tf
-5.7874 -1.5023 Td
(Case)Tj
2.1732 0 Td
(study)Tj
2.504 0 Td
(strategy)Tj
3.5338 0 Td
(developed)Tj
4.4268 0 Td
(for)Tj
1.4693 0 Td
(the)Tj
1.5402 0 Td
(assessment)Tj
4.819 0 Td
(of)Tj
1.0677 0 Td
(the)Tj
1.5401 0 Td
(contamination)Tj
-23.0741 -1.167 Td
(level)Tj
2.1071 0 Td
(of)Tj
1.0677 0 Td
(cyanobacteria)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 317.0267 cm
BT
/F7 1 Tf
1 TL
-0.004 Tc
0 0 Td
(To)Tj
1.3379 0 Td
(evaluate)Tj
3.4582 0 Td
(the)Tj
1.474 0 Td
(contamination)Tj
6.1172 0 Td
(status)Tj
2.5001 0 Td
(of)Tj
1.0148 0 Td
(public)Tj
2.7099 0 Td
(cyanobacterial)Tj
5.9924 0 Td
(genome)Tj
3.4072 0 Td
(assemblies,)Tj
4.6488 0 Td
(we)Tj
1.3323 0 Td
(imple-)Tj
-33.9928 -1.3039 Td
(mented)Tj
3.2598 0 Td
(a)Tj
0.6519 0 Td
(strategy)Tj
3.3279 0 Td
(based)Tj
2.4718 0 Td
(on)Tj
1.2756 0 Td
(combining)Tj
4.5751 0 Td
(evidence)Tj
3.7133 0 Td
(across)Tj
2.6759 0 Td
(multiple)Tj
3.566 0 Td
(independent)Tj
5.278 0 Td
(methods)Tj
3.6851 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(Fig)Tj
1.8198 0 Td
(1)Tj
0 g
(\).)Tj
-36.3002 -1.2982 Td
(The)Tj
1.7801 0 Td
(rationale)Tj
3.753 0 Td
(was)Tj
1.6952 0 Td
(that,)Tj
2.0069 0 Td
(given)Tj
2.3754 0 Td
(the)Tj
1.474 0 Td
(complexity)Tj
4.6431 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4683 0 Td
(task,)Tj
2.0353 0 Td
(no)Tj
1.2756 0 Td
(single)Tj
2.5285 0 Td
(method)Tj
3.3278 0 Td
(would)Tj
2.7099 0 Td
(be)Tj
1.1509 0 Td
(expected)Tj
-33.2388 -1.2983 Td
(to)Tj
1.0261 0 Td
(reach)Tj
2.3981 0 Td
(both)Tj
2.0579 0 Td
(maximal)Tj
3.7077 0 Td
(sensitivity)Tj
4.2236 0 Td
(and)Tj
1.7291 0 Td
(specificity.)Tj
4.4334 0 Td
(Moreover,)Tj
4.3993 0 Td
(we)Tj
1.3266 0 Td
(were)Tj
2.1203 0 Td
(interested)Tj
4.1669 0 Td
(not)Tj
1.5704 0 Td
(only)Tj
1.9786 0 Td
(in)Tj
-35.138 -1.3039 Td
(quantifying)Tj
4.8245 0 Td
(the)Tj
1.4683 0 Td
(overall)Tj
2.9027 0 Td
(contamination)Tj
6.1228 0 Td
(level)Tj
2.0126 0 Td
(of)Tj
1.0148 0 Td
(cyanobacterial)Tj
5.9924 0 Td
(genomes,)Tj
3.9968 0 Td
(but)Tj
1.5534 0 Td
(also)Tj
1.7688 0 Td
(in)Tj
1.0318 0 Td
(recognizing)Tj
-32.6889 -1.2983 Td
(and)Tj
1.7291 0 Td
(eliminating)Tj
4.8075 0 Td
(foreign)Tj
3.0897 0 Td
(regions)Tj
3.1635 0 Td
(or)Tj
1.0942 0 Td
(scaffolds,)Tj
3.8834 0 Td
(so)Tj
1.0885 0 Td
(as)Tj
1.0148 0 Td
(to)Tj
1.0261 0 Td
(generate)Tj
3.6057 0 Td
(decontaminated)Tj
7.4891 0 Td
(assemblies.)Tj
-31.9916 -1.2982 Td
(Hence,)Tj
3.033 0 Td
(we)Tj
1.3266 0 Td
(first)Tj
1.8028 0 Td
(considered)Tj
4.6035 0 Td
(a)Tj
0.6519 0 Td
(few)Tj
1.6158 0 Td
(reliable)Tj
3.1407 0 Td
(loci,)Tj
1.8879 0 Td
(i.e.,)Tj
1.5874 0 Td
(genes)Tj
2.4434 0 Td
(that)Tj
1.7745 0 Td
(have)Tj
2.0636 0 Td
(an)Tj
1.2019 0 Td
(extremely)Tj
4.1442 0 Td
(low)Tj
1.6555 0 Td
(probability)Tj
-32.9327 -1.304 Td
(of)Tj
1.0147 0 Td
(horizontal)Tj
4.337 0 Td
(gene)Tj
2.0806 0 Td
(transfer)Tj
3.3166 0 Td
(\(HGT\),)Tj
3.2201 0 Td
(such)Tj
2.0636 0 Td
(as)Tj
1.0148 0 Td
(SSU)Tj
1.9049 0 Td
(rRNA)Tj
2.6362 0 Td
(\(16S\))Tj
2.3244 0 Td
(and)Tj
1.7291 0 Td
(ribosomal)Tj
4.2406 0 Td
(proteins.)Tj
3.7417 0 Td
(We)Tj
1.6101 0 Td
(used)Tj
-35.2344 -1.2982 Td
(RNAmmer/SINA)Tj
7.2623 0 Td
([)Tj
0.83 0.64 0.02 0 k
(32)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
(33)Tj
0 g
(],)Tj
3.2541 0 Td
(an)Tj
1.2019 0 Td
(approach)Tj
3.9515 0 Td
(based)Tj
2.4718 0 Td
(on)Tj
1.2756 0 Td
(a)Tj
0.6519 0 Td
(reference)Tj
3.9175 0 Td
(SSU)Tj
1.9105 0 Td
(rRNA)Tj
2.6305 0 Td
(\(16S\))Tj
2.3301 0 Td
(database,)Tj
3.8608 0 Td
(and)Tj
-34.7185 -1.2983 Td
(42,)Tj
2.1769 0 Td
(a)Tj
0.6577 0 Td
(BLASTX-based)Tj
6.3666 0 Td
(program)Tj
3.702 0 Td
(coupled)Tj
3.3959 0 Td
(with)Tj
1.9955 0 Td
(a)Tj
0.652 0 Td
(reference)Tj
3.9175 0 Td
(ribosomal)Tj
4.2406 0 Td
(protein)Tj
3.1521 0 Td
(database)Tj
3.6396 0 Td
(to)Tj
1.0262 0 Td
(detect)Tj
-34.9226 -1.3039 Td
(sequences)Tj
4.2179 0 Td
(in)Tj
1.0374 0 Td
(cyanobacterial)Tj
5.9925 0 Td
(genomes)Tj
3.7643 0 Td
(that)Tj
1.7802 0 Td
(are)Tj
1.4513 0 Td
(phylogenetically)Tj
6.7011 0 Td
(related)Tj
2.948 0 Td
(to)Tj
1.0205 0 Td
(non-cyanobacterial)Tj
-28.9132 -1.2983 Td
(organisms.)Tj
4.5694 0 Td
(Second,)Tj
3.3392 0 Td
(we)Tj
1.3152 0 Td
(used)Tj
2.0523 0 Td
(CheckM)Tj
3.6397 0 Td
([)Tj
0.83 0.64 0.02 0 k
(14)Tj
0 g
(],)Tj
2.0636 0 Td
(a)Tj
0.6463 0 Td
(comprehensive)Tj
6.2758 0 Td
(package)Tj
3.4016 0 Td
(based)Tj
2.4661 0 Td
(on)Tj
1.2643 0 Td
(the)Tj
1.457 0 Td
(phylogenetic)Tj
-32.4905 -1.2982 Td
(labelling)Tj
3.5999 0 Td
(of)Tj
1.0148 0 Td
(lineage-specific)Tj
6.3496 0 Td
(marker)Tj
3.1408 0 Td
(genes,)Tj
2.6645 0 Td
(thereby)Tj
3.2258 0 Td
(allowing)Tj
3.617 0 Td
(us)Tj
1.1112 0 Td
(to)Tj
1.0261 0 Td
(probe)Tj
2.5455 0 Td
(a)Tj
0.652 0 Td
(larger)Tj
2.5341 0 Td
(part)Tj
1.8425 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4684 0 Td
(cya-)Tj
-35.807 -1.2983 Td
(nobacterial)Tj
4.6771 0 Td
(assemblies.)Tj
4.6488 0 Td
(Third,)Tj
2.7552 0 Td
(we)Tj
1.3266 0 Td
(explored)Tj
3.7021 0 Td
(three)Tj
2.262 0 Td
(genome-wide)Tj
5.6636 0 Td
(methods)Tj
3.6793 0 Td
(to)Tj
1.0262 0 Td
(maximize)Tj
4.1329 0 Td
(our)Tj
-33.8738 -1.3039 Td
(detection)Tj
3.9344 0 Td
(power.)Tj
2.948 0 Td
(We)Tj
1.6101 0 Td
(investigated)Tj
4.9889 0 Td
(their)Tj
2.109 0 Td
(parameterization)Tj
7.0469 0 Td
(by)Tj
1.1849 0 Td
(comparing)Tj
4.5694 0 Td
(their)Tj
2.1089 0 Td
(results)Tj
2.812 0 Td
(with)Tj
1.9956 0 Td
(those)Tj
-35.3081 -1.2983 Td
(based)Tj
2.4717 0 Td
(on)Tj
1.2756 0 Td
(ribosomal)Tj
4.2406 0 Td
(genes,)Tj
2.6646 0 Td
(considered)Tj
4.6034 0 Td
(as)Tj
1.0148 0 Td
(the)Tj
1.4684 0 Td
(gold)Tj
1.9672 0 Td
(standard.)Tj
3.9458 0 Td
(Hence,)Tj
3.033 0 Td
(we)Tj
1.3266 0 Td
(tested)Tj
2.5512 0 Td
(Kraken)Tj
3.1691 0 Td
([)Tj
0.83 0.64 0.02 0 k
(34)Tj
0 g
(],)Tj
2.0806 0 Td
(a)Tj
-35.8126 -1.2982 Td
(widely)Tj
2.8232 0 Td
(used)Tj
2.058 0 Td
(metagenomic)Tj
5.6522 0 Td
(classifier)Tj
3.6624 0 Td
(based)Tj
2.4718 0 Td
(on)Tj
1.2755 0 Td
(long)Tj
1.9843 0 Td
(\(signature\))Tj
4.5977 0 Td
(DNA)Tj
2.3811 0 Td
(kmers)Tj
2.6873 0 Td
(\(2131)Tj
2.982 0 Td
(nt\),)Tj
1.6327 0 Td
(against)Tj
-34.2082 -1.304 Td
(a)Tj
0.6519 0 Td
(curated)Tj
3.2258 0 Td
(reference)Tj
3.9175 0 Td
(database)Tj
3.6396 0 Td
(derived)Tj
3.2145 0 Td
(from)Tj
2.2053 0 Td
(Ensembl)Tj
3.6964 0 Td
(Bacteria,)Tj
3.6793 0 Td
(and)Tj
1.7292 0 Td
(CONCOCT)Tj
5.0513 0 Td
([)Tj
0.83 0.64 0.02 0 k
(35)Tj
0 g
(],)Tj
2.0749 0 Td
(a)Tj
0.652 0 Td
(short)Tj
-33.7377 -1.2982 Td
(DNA)Tj
2.3754 0 Td
(kmer)Tj
2.33 0 Td
(\(46)Tj
2.0296 0 Td
(nt\))Tj
1.406 0 Td
(metagenomic)Tj
5.6522 0 Td
(binning)Tj
3.3733 0 Td
(package)Tj
3.4128 0 Td
(that)Tj
1.7745 0 Td
(does)Tj
2.041 0 Td
(not)Tj
1.576 0 Td
(require)Tj
3.1124 0 Td
(a)Tj
0.652 0 Td
(reference)Tj
3.9175 0 Td
(database,)Tj
ET
Q
q
1 j
1 J
0 w
576 737.1 m
36 737.1 l
36 737.6 l
576 737.6 l
f*
36 741.2598 107.1496 23.6976 re
W* n
q
107.0929 0 0 23.6409 36 741.3165 cm
q
/I0 Do
Q
Q
Q
q
0 0 612 792 re
W* n
1 j
1 J
0 w
7.9999 0 0 7.9999 412.6677 745.7952 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(Contam)Tj
3.4441 0 Td
(ination)Tj
3.1039 0 Td
(level)Tj
2.2323 0 Td
(of)Tj
1.0418 0 Td
(cyanobac)Tj
4.2024 0 Td
(terial)Tj
2.3386 0 Td
(genomes)Tj
ET
Q
q
1 j
1 J
0 w
36 48.0002 m
576 48.0002 l
576 47.5002 l
36 47.5002 l
f*
0.83 0.64 0.02 0 k
81.5811 34.9228 m
237.8835 34.9228 l
h
f*
0 g
7.9999 0 0 7.9999 36 36 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(PLOS)Tj
2.8559 0 Td
(ONE)Tj
2.3669 0 Td
(|)Tj
0.83 0.64 0.02 0 k
0.4748 0 Td
(https://doi.or)Tj
5.4142 0 Td
(g/10.137)Tj
3.8198 0 Td
(1/journal.po)Tj
5.1236 0 Td
(ne.02003)Tj
4.089 0 Td
(23)Tj
0 g
2.0906 0 Td
(July)Tj
1.9701 0 Td
(25,)Tj
1.5874 0 Td
(2018)Tj
35.3483 0 Td
(3)Tj
0.7654 0 Td
(/)Tj
ET
endstream
endobj
94 0 obj
<>stream
endstream
endobj
95 0 obj
<>stream
endstream
endobj
96 0 obj
<>stream
endstream
endobj
97 0 obj
<>stream
endstream
endobj
98 0 obj
<>stream
endstream
endobj
99 0 obj
<>stream
endstream
endobj
100 0 obj
<>stream
endstream
endobj
101 0 obj
<>stream
endstream
endobj
102 0 obj
<>stream
endstream
endobj
103 0 obj
<>stream
endstream
endobj
104 0 obj
<>stream
endstream
endobj
105 0 obj
<>stream
endstream
endobj
106 0 obj
<>stream
endstream
endobj
107 0 obj
<>stream
endstream
endobj
108 0 obj
<>stream
endstream
endobj
109 0 obj
<>stream
endstream
endobj
110 0 obj
<>stream
endstream
endobj
111 0 obj
<>stream
BT
66.402 0 Td
(26)Tj
ET
Q
endstream
endobj
112 0 obj
<>/XObject<>>>/CropBox[0 0 612 792]/MediaBox[0 0 612 792]/Parent 11 0 R/Annots 114 0 R/Contents 115 0 R/TrimBox[0 0 612 792]>>
endobj
113 0 obj
<>stream
x콅{I?r羟{5Ylqw]Hww d2KH2 kݞJwշN:uηNA@A@"W/ܼvG}dVYtVX>Ȩ,w8z~ҠW.لR2
g^xWᱻ,wWzf
`OɈM:͋gldjġ[~لW+m]go_͠7=jOY4.o߾C?}x+L̀G7{hAA@A@AGܼtNV.2Žv^ӄ>=Ow @& = o$Ŀ=]O]8τέ6G+
-3hȧE[=i )x6aRՋ5#^/$翢Wq;o]0o(%㭠d]7cguqUl?gxփW=6#zF4GQ3[3b@"a
*MGئtnڽkV]TKQgfibuzaMZn:=/FRMrW*V-||K?N !gOݨZ`/~q/ʹnػW/yvsA{C}hU4
GͤnmN'}#gO?ݛo%~o^|}&