A miRNA catalog and ncRNA annotation of the short-living fish Nothobranchius furzeri

Supplemental Material

M. Baumgart, E. Barth, A. Savino, M. Groth, P. Koch, A. Petzold, I. Arisi, M. Platzer, M. Marz and A. Cellerino

 

Contents

Data

small RNA-Seq data

Supplement Table 1: General Information about the small RNA-Seq libraries, as well as some mapping statistics.
Sample Read Numbers FastQC read statistics Read count distribution Used for mirDeep* search
raw trimmed raw trimmed
nfu_brain_grz_5_JG20_1 12,734,938 11,762,112 fastq report fastq report file yes
nfu_brain_grz_5_JG21_1 15,426,423 14,031,891 fastq report fastq report file yes
nfu_brain_grz_5_JG23_1 10,948,323 10,111,076 fastq report fastq report file yes
nfu_brain_grz_5_JG25_1 13,097,325 10,332,918 fastq report fastq report file yes
nfu_brain_grz_5_JG35_1 7,418,746 6,675,144 fastq report fastq report file yes
nfu_liver_grz_5_JG17_3 8,408,462 5,366,316 fastq report fastq report file yes
nfu_liver_grz_5_JG22_3 12,253,940 7,444,996 fastq report fastq report file yes
nfu_liver_grz_5_JG23_3 10,911,962 8,385,803 fastq report fastq report file yes
nfu_liver_grz_5_JG25_3 10,760,322 7,051,563 fastq report fastq report file yes
nfu_liver_grz_5_JG35_3 9,671,209 6,206,133 fastq report fastq report file yes
nfu_skin_grz_5_JG18_5 15,250,809 12,160,710 fastq report fastq report file no
nfu_skin_grz_5_JG19_5 13,142,159 9,857,454 fastq report fastq report file no
nfu_skin_grz_5_JG21_5 13,864,019 10,643,482 fastq report fastq report file no
nfu_skin_grz_5_JG25_5 24,257,944 20,809,019 fastq report fastq report file no
nfu_skin_grz_5_JG35_5 13,283,992 11,466,251 fastq report fastq report file no
nfu_brain_grz_7_JG48_1 14,339,608 11,729,366 fastq report fastq report file yes
nfu_brain_grz_7_JG53_1 20,926,796 18,840,589 fastq report fastq report file yes
nfu_brain_grz_7_JG55_1 24,787,216 18,588,937 fastq report fastq report file yes
nfu_brain_grz_7_JG64_1 14,066,197 13,093,979 fastq report fastq report file yes
nfu_brain_grz_7_JG65_1 18,220,188 14,944,024 fastq report fastq report file yes
nfu_liver_grz_7_JG48_3 9,203,104 7,153,097 fastq report fastq report file yes
nfu_liver_grz_7_JG53_3 10,446,133 6,327,722 fastq report fastq report file yes
nfu_liver_grz_7_JG55_3 9,550,646 5,783,205 fastq report fastq report file no
nfu_liver_grz_7_JG64_3 7,887,036 4,717,950 fastq report fastq report file yes
nfu_liver_grz_7_JG65_3 9,903,472 5,868,603 fastq report fastq report file yes
nfu_skin_grz_7_JG48_5 18,161,324 15,389,947 fastq report fastq report file yes
nfu_skin_grz_7_JG53_5 19,916,395 15,865,845 fastq report fastq report file yes
nfu_skin_grz_7_JG55_5 30,562,673 26,255,677 fastq report fastq report file no
nfu_skin_grz_7_JG64_5 17,750,499 14,433,654 fastq report fastq report file yes
nfu_skin_grz_7_JG65_5 26,448,321 20,617,501 fastq report fastq report file yes
nfu_brain_grz_10_JG57_1 30,384,028 28,441,528 fastq report fastq report file yes
nfu_brain_grz_10_JG58_1 21,487,722 19,885,349 fastq report fastq report file yes
nfu_brain_grz_10_JG59_1 22,868,403 19,328,687 fastq report fastq report file no
nfu_brain_grz_10_JG60_1 21,705,768 20,135,638 fastq report fastq report file yes
nfu_brain_grz_10_JG62_1 21,347,226 19,317,934 fastq report fastq report file yes
nfu_liver_grz_10_JG57_3 11,573,653 8,762,785 fastq report fastq report file no
nfu_liver_grz_10_JG58_3 8,815,974 6,215,718 fastq report fastq report file no
nfu_liver_grz_10_JG59_3 13,869,623 8,772,020 fastq report fastq report file no
nfu_liver_grz_10_JG60_3 12,031,199 7,666,964 fastq report fastq report file yes
nfu_liver_grz_10_JG62_3 12,485,151 7,774,991 fastq report fastq report file yes
nfu_skin_grz_10_JG57_5 25,404,639 19,672,059 fastq report fastq report file no
nfu_skin_grz_10_JG58_5 26,147,567 20,963,316 fastq report fastq report file no
nfu_skin_grz_10_JG59_5 27,791,380 23,465,290 fastq report fastq report file no
nfu_skin_grz_10_JG60_5 25,985,715 21,498,364 fastq report fastq report file yes
nfu_skin_grz_10_JG61_5 17,821,189 15,952,395 fastq report fastq report file no
nfu_brain_grz_12_JG10_1 15,812,965 13,976,652 fastq report fastq report file no
nfu_brain_grz_12_JG11_1 19,671,017 16,466,547 fastq report fastq report file no
nfu_brain_grz_12_JG13_1 17,026,839 15,688,839 fastq report fastq report file no
nfu_brain_grz_12_JG14_1 21,878,886 20,211,456 fastq report fastq report file no
nfu_brain_grz_12_JG15_1 23,649,284 21,767,750 fastq report fastq report file yes
nfu_liver_grz_12_JG10_3 9,932,004 6,894,928 fastq report fastq report file yes
nfu_liver_grz_12_JG11_3 8,586,341 5,287,151 fastq report fastq report file yes
nfu_liver_grz_12_JG13_3 7,947,694 5,702,003 fastq report fastq report file yes
nfu_liver_grz_12_JG14_3 8,847,751 5,680,710 fastq report fastq report file yes
nfu_liver_grz_12_JG15_3 13,676,487 10,993,249 fastq report fastq report file yes
nfu_skin_grz_12_JG13_5 17,019,232 15,269,022 fastq report fastq report file yes
nfu_skin_grz_12_JG14_5 14,384,468 13,316,531 fastq report fastq report file yes
nfu_skin_grz_12_JG5_5 23,144,769 20,738,307 fastq report fastq report file no
nfu_skin_grz_12_JG6_5 18,049,762 16,477,741 fastq report fastq report file no
nfu_skin_grz_12_JG7_5 10,060,042 8,851,300 fastq report fastq report file no
nfu_brain_grz_14_JG66_1 22,668,120 21,252,536 fastq report fastq report file no
nfu_brain_grz_14_JG69_1 24,237,684 22,464,782 fastq report fastq report file no
nfu_brain_grz_14_JG70_1 21,665,478 20,509,255 fastq report fastq report file yes
nfu_brain_grz_14_JG72_1 17,409,524 16,252,111 fastq report fastq report file no
nfu_brain_grz_14_JG73_1 18,779,293 15,679,790 fastq report fastq report file yes
nfu_liver_grz_14_JG67_3 11,471,101 7,611,045 fastq report fastq report file yes
nfu_liver_grz_14_JG68_3 6,552,147 3,982,705 fastq report fastq report file no
nfu_liver_grz_14_JG70_3 23,503,329 11,108,685 fastq report fastq report file yes
nfu_liver_grz_14_JG71_3 10,232,907 5,872,087 fastq report fastq report file yes
nfu_liver_grz_14_JG73_3 12,976,646 10,096,571 fastq report fastq report file yes
nfu_skin_grz_14_JG66_5 15,203,441 13,218,557 fastq report fastq report file yes
nfu_skin_grz_14_JG67_5 12,448,973 10,546,826 fastq report fastq report file yes
nfu_skin_grz_14_JG68_5 32,251,959 27,861,305 fastq report fastq report file no
nfu_skin_grz_14_JG69_5 54,785,286 46,275,011 fastq report fastq report file no
nfu_skin_grz_14_JG70_5 29,370,356 24,716,109 fastq report fastq report file yes
nfu_brain_mzm_5_JM96_1 3,330,320 2,851,326 fastq report fastq report file no
nfu_brain_mzm_5_JM97_1 5,303,425 4,834,088 fastq report fastq report file no
nfu_brain_mzm_5_JM101_1 2,126,388 1,830,792 fastq report fastq report file no
nfu_brain_mzm_5_JM103_1 4,277,442 3,886,465 fastq report fastq report file no
nfu_liver_mzm_5_JM100_3 13,019,600 11,358,783 fastq report fastq report file yes
nfu_liver_mzm_5_JM101_3 10,574,364 8,876,538 fastq report fastq report file yes
nfu_liver_mzm_5_JM103_3 11,281,090 9,885,866 fastq report fastq report file yes
nfu_liver_mzm_5_JM97_3 12,040,747 9,778,732 fastq report fastq report file yes
nfu_liver_mzm_5_JM98_3 13,029,620 10,825,385 fastq report fastq report file yes
nfu_skin_mzm_5_JM100_5 9,577,170 8,038,166 fastq report fastq report file yes
nfu_skin_mzm_5_JM102_5 14,214,297 11,543,345 fastq report fastq report file no
nfu_skin_mzm_5_JM103_5 14,729,279 11,873,861 fastq report fastq report file yes
nfu_skin_mzm_5_JM94_5 13,116,619 11,436,605 fastq report fastq report file yes
nfu_skin_mzm_5_JM95_5 17,635,457 13,849,408 fastq report fastq report file yes
nfu_brain_mzm_12_JM105_1 6,115,675 5,586,081 fastq report fastq report file yes
nfu_brain_mzm_12_JM107_1 6,353,160 5,467,109 fastq report fastq report file yes
nfu_brain_mzm_12_JM109_1 6,610,788 6,174,886 fastq report fastq report file yes
nfu_brain_mzm_12_JM113_1 2,748,938 2,378,628 fastq report fastq report file yes
nfu_liver_mzm_12_JM104_3 13,196,782 9,356,132 fastq report fastq report file yes
nfu_liver_mzm_12_JM105_3 11,501,269 9,732,734 fastq report fastq report file yes
nfu_liver_mzm_12_JM106_3 12,340,239 8,520,685 fastq report fastq report file yes
nfu_liver_mzm_12_JM107_3 10,110,895 8,367,930 fastq report fastq report file yes
nfu_liver_mzm_12_JM115_3 15,583,525 13,039,666 fastq report fastq report file yes
nfu_skin_mzm_12_JM104_5 15,532,860 14,161,506 fastq report fastq report file yes
nfu_skin_mzm_12_JM105_5 20,562,609 17,944,313 fastq report fastq report file yes
nfu_skin_mzm_12_JM109_5 24,519,560 21,603,540 fastq report fastq report file no
nfu_skin_mzm_12_JM110_5 19,121,632 14,695,169 fastq report fastq report file no
nfu_skin_mzm_12_JM116_5 36,614,126 32,007,277 fastq report fastq report file no
nfu_brain_mzm_20_JM75_1 4,009,122 3,590,461 fastq report fastq report file yes
nfu_brain_mzm_20_JM79_1 3,729,573 3,304,284 fastq report fastq report file yes
nfu_brain_mzm_20_JM84_1 3,561,242 3,335,455 fastq report fastq report file yes
nfu_brain_mzm_20_JM86_1 8,247,045 7,586,710 fastq report fastq report file yes
nfu_liver_mzm_20_JM75_3 13,806,887 11,401,962 fastq report fastq report file yes
nfu_liver_mzm_20_JM79_3 9,975,410 8,080,584 fastq report fastq report file yes
nfu_liver_mzm_20_JM82_3 14,965,556 11,861,964 fastq report fastq report file yes
nfu_liver_mzm_20_JM84_3 13,844,364 11,148,527 fastq report fastq report file yes
nfu_liver_mzm_20_JM85_3 18,907,229 16,845,900 fastq report fastq report file yes
nfu_skin_mzm_20_JM79_5 25,362,287 21,818,342 fastq report fastq report file yes
nfu_skin_mzm_20_JM84_5 22,354,473 20,117,287 fastq report fastq report file yes
nfu_skin_mzm_20_JM87_5 17,768,256 14,205,983 fastq report fastq report file no
nfu_skin_mzm_20_JM88_5 9,942,880 8,926,381 fastq report fastq report file no
nfu_skin_mzm_20_JM91_5 24,434,867 18,884,143 fastq report fastq report file no
nfu_brain_mzm_27_JM52_1 6,869,923 6,200,725 fastq report fastq report file no
nfu_brain_mzm_27_JM62_1 4,650,937 4,262,072 fastq report fastq report file no
nfu_brain_mzm_27_JM66_1 2,266,482 2,931,890 fastq report fastq report file no
nfu_brain_mzm_27_JM72_1 3,385,298 1,897,048 fastq report fastq report file no
nfu_liver_mzm_27_JM61_3 17,100,867 13,319,258 fastq report fastq report file yes
nfu_liver_mzm_27_JM69_3 10,011,929 7,257,793 fastq report fastq report file yes
nfu_liver_mzm_27_JM72_3 12,510,422 9,323,519 fastq report fastq report file yes
nfu_liver_mzm_27_JM74_3 10,415,044 8,480,329 fastq report fastq report file yes
nfu_liver_mzm_27_JM83_3 15,193,692 11,808,026 fastq report fastq report file yes
nfu_skin_mzm_27_JM55_5 16,399,422 14,534,573 fastq report fastq report file no
nfu_skin_mzm_27_JM62_5 9,725,265 8,598,497 fastq report fastq report file yes
nfu_skin_mzm_27_JM66_5 19,569,448 17,262,823 fastq report fastq report file yes
nfu_skin_mzm_27_JM72_5 15,513,448 14,306,782 fastq report fastq report file yes
nfu_skin_mzm_27_JM73_5 14,306,216 11,293,782 fastq report fastq report file yes
nfu_brain_mzm_32_JM27_1 3,813,639 3,415,215 fastq report fastq report file yes
nfu_brain_mzm_32_JM29_1 3,935,180 3,683,254 fastq report fastq report file yes
nfu_brain_mzm_32_JM31_1 7,480,657 6,885,349 fastq report fastq report file yes
nfu_brain_mzm_32_JM50_1 6,700,352 6,127,408 fastq report fastq report file yes
nfu_brain_mzm_32_JM77_1 6,720,802 6,218,651 fastq report fastq report file yes
nfu_brain_mzm_39_JM13_1 3,720,410 3,305,898 fastq report fastq report file yes
nfu_brain_mzm_39_JM15_1 4,346,512 3,804,979 fastq report fastq report file yes
nfu_brain_mzm_39_JM18_1 4,273,301 3,944,690 fastq report fastq report file yes
nfu_brain_mzm_39_JM1_1 2,897,196 2,439,413 fastq report fastq report file no
nfu_liver_mzm_39_JM12_3 10,390,732 8,216,247 fastq report fastq report file yes
nfu_liver_mzm_39_JM13_3 11,003,172 8,567,777 fastq report fastq report file yes
nfu_liver_mzm_39_JM15_3 10,595,612 8,672,903 fastq report fastq report file yes
nfu_liver_mzm_39_JM18_3 11,665,645 8,823,320 fastq report fastq report file yes
nfu_liver_mzm_39_JM1_3 14,180,611 10,570,854 fastq report fastq report file yes
nfu_skin_mzm_39_JM24_5 15,221,734 11,647,208 fastq report fastq report file no
nfu_skin_mzm_39_JM1_5 71,406,376 63,144,669 fastq report fastq report file no
nfu_skin_mzm_39_JM13_5 11,743,610 10,153,212 fastq report fastq report file no
nfu_skin_mzm_39_JM15_5 42,824,201 36,298,333 fastq report fastq report file no
nfu_skin_mzm_39_JM18_5 15,354,083 12,635,926 fastq report fastq report file no
nfu_mzm_embryo_0403_som 3,516,736 2,479,827 fastq report fastq report - yes
nfu_mzm_embryo_0403_24_hpf 5,404,054 2,282,133 fastq report fastq report - yes
nfu_mzm_embryo_SNo_37 33,287,472 13,889,053 fastq report fastq report - yes
nfu_mzm_embryo_pool3_index1 32,512,915 25,205,272 fastq report fastq report - yes
nfu_mzm_embryo_pool3_index3 7,725,748 6,315,990 fastq report fastq report - yes
nfu_mzm_embryo_pool3_index4 14,722,676 11,719,465 fastq report fastq report - yes
nfu_mzm_embryo_pool3_index5 36,800,770 23,300,190 fastq report fastq report - yes
nko_brain_26 24,573,483 24,402,770 fastq report fastq report - no
nkor_brain_28 21,117,057 20,920,195 fastq report fastq report - no
npie_brain_56 24,298,361 24,038,395 fastq report fastq report - no
npie_brain_57 29,681,279 29,120,780 fastq report fastq report - no
nkun_brain_74 20,525,653 20,337,189 fastq report fastq report - no
nkun_brain_75 25,483,001 25,251,035 fastq report fastq report - no
nkad_brain_B1 18,120,615 17,780,025 fastq report fastq report - no
nkad_brain_B2 23,374,378 23,019,985 fastq report fastq report - no
nrac_brain_B3 18,743,522 18,455,871 fastq report fastq report - no
nrac_brain_B4 16,749,028 16,449,616 fastq report fastq report - no
astr_brain_P1 36,094,841 35,203,627 fastq report fastq report - no
astr_brain_P2 35,095,345 34,655,232 fastq report fastq report - no
 

Results

MiRNA and ncRNA annotations

Supplementary material 1: ncRNA annotation

Supplementary material 2: miRNA annotation

PCA Plots

Supplement Table 2: Principle Componant Analysis (PCA) plots based on the normalized read counts of the 750 most variable genes of the respective tissue or timepoint comparisons of Nothobranchius furzeri GRZ and Nothobranchius furzeri MZM.
GRZ MZM
Preview Description Download Preview Description Download
PCA plot of the Nothobranchius furzeri GRZ small RNA-Seq samples, including all tissues (brain, liver skin) and all timepoints (5, 7, 10, 12, 14 weeks). pdf PCA plot of the Nothobranchius furzeri MZM small RNA-Seq samples, including all tissues (brain, liver skin) and all timepoints (5, 12, 20, 27, 39 weeks). pdf
Three-dimensional PCA plot of the Nothobranchius furzeri GRZ small RNA-Seq samples, including all tissues (brain, liver skin) and all timepoints (5, 7, 10, 12, 14 weeks). pdf Three-dimensional PCA plot of the Nothobranchius furzeri MZM small RNA-Seq samples, including all tissues (brain, liver skin) and all timepoints (5, 12, 20, 27, 39 weeks). pdf
PCA plot of the Nothobranchius furzeri GRZ brain small RNA-Seq samples, including all timepoints (5, 7, 10, 12, 14 weeks). pdf PCA plot of the Nothobranchius furzeri MZM brain small RNA-Seq samples, including all timepoints (5, 12, 20, 27, 39 weeks). pdf
PCA plot of the Nothobranchius furzeri GRZ liver small RNA-Seq samples, including all timepoints (5, 7, 10, 12, 14 weeks). pdf PCA plot of the Nothobranchius furzeri MZM liver small RNA-Seq samples, including all timepoints (5, 12, 20, 27, 39 weeks). pdf
PCA plot of the Nothobranchius furzeri GRZ skin small RNA-Seq samples, including all timepoints (5, 7, 10, 12, 14 weeks). pdf PCA plot of the Nothobranchius furzeri MZM skin small RNA-Seq samples, including all timepoints (5, 7, 10, 12, 14 weeks). pdf
 

Expressed miRNAs in closely related killifish

Supplement Table 3: Based on the identified expressed miRNAs a phylogenie of the seven killifish A. striatum, N. kadleci, N. rachovii, N. pienaari, N. kunthae, N. korthausae and N. furzeriwas calculated via hierarchical clustering.
Expressed Nfu miRNAs Expressed miRBase miRNAs
Aphyosemion striatum Aphyosemion striatum
Nothobranchius pienaari Nothobranchius pienaari
Nothobranchius korthausae Nothobranchius korthausae
Nothobranchius rachovii Nothobranchius rachovii
Nothobranchius kunthae Nothobranchius kunthae
Nothobranchius kadleci Nothobranchius kadleci
Nothobranchius furzeri Nothobranchius furzeri
 

miRNA clusters and miRNA family assignments in different fish species

Supplement Table 4: For the four well-known fish Danio rerio, Oryzia latipes, Takifugu rupripes and Gasterosteus aculeatus, as well as N. furzeri, we tried to assigend each known miRNA to an MirBase family and calculated miRNA clusters through their genomes.
Species miRNA cluster miRNA family assignments
Nothobranchius furzeri cluster list miRNA assignments
Danio rerio cluster list miRNA assignments
Oryzia latipes cluster list miRNA assignments
Takifugu rupripes cluster list miRNA assignments
Gasterosteus aculeatus cluster list miRNA assignments

ncRNA Alignments

Supplement Table 5: Listed here are all additionally identified ncRNAs of N. furzeri, with their corresponding names, RFAM numbers and sequences in the Stockholm alignment format.
ncRNA class RFAM ID Alignment ncRNA class RFAM ID Alignment
5S rRNA RF00001 stk 7SK RF00100 stk
5.8S rRNA RF00002 stk Vimentin3 RF00109 stk
U1 RF00003 stk CAESAR RF00172 stk
U2 RF00004 stk Antizyme FSE RF00381 stk
Vault RF00006 stk U1A_PIE RF00460 stk
U12 RF00007 stk K_chan_RES RF00485 stk
RNase P RF00009 stk U11 RF00548 stk
U4 RF00015 stk U4atac RF00618 stk
SRP RF00017 stk U6atac RF00619 stk
Y RNA RF00019 stk DPB RF01455 stk
U5 RF00020 stk mascRNA-menRNA RF01684 stk
U11 RF00024 stk GABA3 RF01803 stk
U6 RF00026 stk SPRY4-IT_1 RF02038 stk
RNase MRP RF00030 stk SPRY4-IT_2 RF02039 stk
IRE1 RF00037 stk MEG8_1 RF02145 stk
TPP RF00059 stk MEG8_3 RF02147 stk
U7 RF00066 stk

miRNA target prediction and enrichment analysis

miRNA target prediction

conservative target prediction: file non-conservative target prediction: file
miRNA seed regions: file 3' UTR alignments: file TargetScan N. furzeri & D. rerio output: file TargetScan N. furzeri, D. rerio, M. musculus & H. sapiens output: file

miRNA target enrichment analysis

In the study Baumgart, Mario, et al. "RNA-Seq of the aging brain in the short-lived fish N. furzeri-conserved pathways and novel genes associated with neurogenesis." Aging Cell 13.6 (2014) we described two sets of genes, being constantly down-regulated in the aging brain of N. furzeri, namely cluster 1 and cluster 5. Enrichment scores for all candidate miRNAs for both sets can be found here: cluster 1 cluster 5
In the study Reichwald, Kathrin, et al. "Insights into sex chromosome evolution and aging from the genome of a short-lived fish." Cell 163.6 (2015) we provide, for three different tissues, sets of genes, being down-regulated in very old N. furzeri individuals compared to young ones. Enrichment scores for all candidate miRNAs for the three tissues brain, liver, skin can be found here: brain liver skin