Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (Physeter macrocephalus)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animal and Tissue Collection
2.2. RNA Extraction and Quantification
2.3. PacBio Iso-Seq Library Preparation and Sequencing
2.4. RNA-seq Library Preparation and Sequencing
2.5. Bioinformatics Analysis of PacBio Data and RNA-seq Data
2.6. Quantification and Annotation of Gene Expression Levels
2.7. Sequence Analysis
3. Results
3.1. Full-Length Transcripts from the Skin of Sperm Whale
3.2. Annotations and Analysis of Full-Length Transcriptome
3.3. Enrichment of Immune-Related Pathways in the Skin of Sperm Whale
3.4. NOD-Like Receptor Signaling Pathway
3.5. Structural and Evolutional Analysis of NOD1 Gene in Sperm Whale
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Species Name | Protein ID | Length (Amino Acids) |
---|---|---|
Tursiops truncatus | XP_019781619.1 | 953 |
Lagnorhynchus obliquidens | XP_026958076.1 | 953 |
Globicephla melas | XP_030713315.1 | 953 |
Orcinus orca | XP_033284214.1 | 953 |
Phocoena sinus | XP_032499084.1 | 972 |
Neophocaena asiaeorientalis | XP_024610766.1 | 963 |
Monodon monoceros | XP_029089062.1 | 953 |
Delphinapterus leucas | XP_022439858.1 | 953 |
Lipotes vexillifer | XP_007466161.1 | 953 |
Physeter macrocephalus | Isoform_6383 | 958 |
Odocoileus virginianus texanus | XP_020748129.1 | 954 |
Balaenoptera acutorostrata | XP_028020573.1 | 818 |
Balaenoptera musculus | XP_036718877.1 | 953 |
Ovis aries | XP_004007979.2 | 954 |
Bubalus bubalis | XP_006055719.1 | 954 |
Bos taurus | XP_005205565.2 | 954 |
Camelus bactrianus | XP_010969658.1 | 953 |
Sus scrofa | NP_001107749.1 | 953 |
Anolis carolinensis | XP_003222248.2 | 950 |
Equus caballus | XP_023495227.1 | 897 |
Tupaia chinensis | ELW67927.1 | 1109 |
Homo sapiens | AAD28350.1 | 953 |
Oryctolagus cuniculus | XP_002713781.1 | 953 |
Mus musculus | AAN52479.1 | 953 |
Ornithorhynchus anatinus | XP_001512159.2 | 950 |
Gallus gallus | NP_001305367.1 | 951 |
Danio rerio | XP_002665106.3 | 940 |
Xenopus tropicalis | XP_031759856.1 | 945 |
Canis lupus familiaris | XP_013974568.1 | 964 |
Vulpes vulpes | XP_025874889.1 | 953 |
Proteins/Enzymes Name | Genes ID in This Transcriptome | *** FPKM (Min–Max) | Sequence Alignment Identity Percentage (%) | ||
---|---|---|---|---|---|
Physeter macrocephalus | Lipotes vexillifer | Tursiops truncatus | |||
Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) | Isoform_6383 Isoform_44218 Isoform_24661 Isoform_40056 | 0.41–7.56 | 100.00 (XP_023984584.1) 100.00 (XP_023984584.1) 100.00 (XP_023984584.1) 92.05 (XP_023984584.1) | 96.41 (XP_007466161.1) 98.94 (XP_007466161.1) 98.52 (XP_007466161.1) 90.73 (XP_007466161.1) | 96.73 (XP_019781619.1) 97.88 (XP_033719017.1) 97.78 (XP_019781638.1) 90.07 (XP_033719017.1) |
Interleukin 6(IL-6) | Isoform_60901 Isoform_23835 | 1.32–1.59 | 100.00 (XP_007105488.3) 100.00 (XP_007105488.3) | NM NM | 100.00 (XP_019778462.1) 100.00 (XP_019778462.1) |
Interleukin 8 (IL-8) | Isoform_34284 | 2.71 | 100.00 (XP_007126317.1) | 98.02 (XP_007467625.1) | 96.04 (NP_001267571.1) |
C–X–C motif chemokine 2 (CXCL2) C–X–C motif chemokine 3 (CXCL3) | Isoform_67128 Isoform_70740 Isoform_34284 Isoform_69403 Isoform_45444 | 0.79–7.18 2.29-3.46 2.29-3.46 | 98.53 (XP_023971193.1) 98.53 (XP_023971193.1) 98.44 (XP_023971204.1) 98.41 (XP_007126322.2) 98.44 (XP_007126322.2) | 96.88 (NP_007463281.1) 96.88 (NP_007463281.1) 96.88 (NP_007463281.1) NM NM | 94.12 (NP_004331677.2) 94.12 (NP_004331677.2) 93.75 (NP_004331677.2) NM NM |
C–C motif chemokine 2 (MCP-1) | Isoform_85283 Isoform_14905 Isoform_68475 | 0.08–3.03 | 100.00 (XP_007467625.1) 91.11 (XP_023983766.1) 98.44 (XP_023983766.1) | 90.36 (XP_007458436.1) 82.22 (XP_007458436.1) 89.80 (XP_007458436.1) | NM NM NM |
Cathelicidin antimicrobial peptide (LL37) | Isoform_27979 Isoform_90183 Isoform_92246 | 0.11–15.39 | 100.00 (XP_007101317.2) 100.00 (XP_007101317.2) 100.00 (XP_007101317.2) | 90.91 (XP_007446211.1) 89.94 (XP_007446211.1) 77.99 (XP_007446211.1) | 93.94 (XP_033720747.1) 88.89 (XP_033720747.1) 90.35 (XP_033720747.1) |
transcription factor AP-1 (AP-1) Interferon α (IFNα) | Isoform_38241 Isoform_63047 Isoform_56853 Isoform_75661 | 0.25–264.37 1.04 | 100.00 (XP_023975690.1) 100.00 (XP_023975690.1) 80.97 (XP_023975690.1) 100.00 (XP_023982688.1) | 100.00 (XP_007462636.1) 100.00 (XP_007462636.1) NM 58.90 (XP_007455007.1) | 100.00 (XP_019797942.2) 100.00 (XP_019797942.2) NM 97.22 (AFH89765.1) |
Receptor-interacting serine/threonine–protein kinase 2 (RIP2) | Isoform_20477 Isoform_25948 Isoform_60840 Isoform_78887 | 0.71–1.52 | 100.00 (XP_023982836.1) 100.00 (XP_023982836.1) 100.00 (XP_023982837.1) 100.00 (XP_023982837.1) | 98.33 (XP_007446375.1) 98.33 (XP_007446375.1) 97.07 (XP_007446375.1) 98.39 (XP_007446375.1) | 97.95 (XP_033699058.1) 97.95 (XP_033699058.1) 96.31 (XP_033699060.1) 98.39 (XP_033699059.1) |
transcription factor p65(RELA) | Isoform_11257 Isoform_15246 Isoform_14067 Isoform_35442 | 0.08–10.86 | 100.00 (XP_023989099.1) 87.06 (XP_023989099.1) 99.64 (XP_007128247.1) 100.00 (XP_007128247.1) | 96.01 (XP_007462051.1) 87.06 (XP_007462053.1) 96.01 (XP_007462052.1) 94.46 (XP_007462051.1) | NM NM NM NM |
Nuclear factor NF-kappa-B p105 subunit (NFKB1) | Isoform_2285 Isoform_78940 | 1.34–3.73 | 100.00 (XP_023982362.1) 100.00 (XP_023982361.1) | 95.21 (XP_007463876.1) 97.52 (XP_007463874.1) | 91.78 (XP_019782050.1) 96.88 (XP_019782049.1) |
Inhibitor of nuclear factor kappa-B kinase subunit β (Ikkβ) | Isoform_16029 Isoform_3742 | 0.64–2.16 | 99.44 (XP_028341955.1) 99.73 (XP_028341955.1) | 97.32 (XP_007455533.1) 98.02 (XP_007455533.1) | 96.78 (XP_033704813.1) 98.02 (XP_033704810.1) |
Inhibitor of nuclear factor kappa-B kinase subunit α (Ikkα) | Isoform_69638 Isoform_28559 | 0.25–3.37 | 100.00 (XP_028337608.1) 100.00 (XP_028337608.1) | 100.00 (XP_007117682.1) 97.84 (XP_007470397.1) | 100.00 (XP_033697982.1) 99.27 (XP_033697983.1) |
NF-kappa-B inhibitor α (NFKBIA) | Isoform_44406 Isoform_62842 Isoform_57121 Isoform_5319 | 0.03–66.12 | 100.00 (XP_007119015.1) 100.00 (XP_007119015.1) 100.00 (XP_007119015.1) 89.70 (XP_007119015.1) | 95.54 (XP_007464888.1) 93.87 (XP_007464888.1) 95.37 (XP_007464888.1) NM | NM NM NM NM |
NF-kappa-B inhibitor β(NFKBIB) | Isoform_64970 Isoform_49218 Isoform_61453 Isoform_30066 | 0.36–16.21 | 100.00 (XP_007114641.1) 99.46 (XP_007114641.2) 100.00 (XP_007114641.2) 100.00 (XP_007114641.2) | 98.58 (XP_007464742.1) 97.27 (XP_007464742.1) 99.08 (XP_007464742.1) 98.71 (XP_007464742.1) | 98.58 (XP_019796701.1) 97.28 (XP_019796701.1) 98.18 (XP_019796701.1) 98.39 (XP_019796701.1) |
Mitogen-activated protein kinase kinase kinase 7 (TAK1) | Isoform_11038 Isoform_3956 Isoform_6441 | 0.39–2.85 | 100.00 (XP_007126290.1) 100.00 (XP_007126290.1) 100.00 (XP_007126290.1) | NM NM NM | NM NM NM |
TAK1-binding protein 3(TAB3) | Isoform_24688 | 1.38 | 99.81 (XP_023972426.1) | 98.85 (XP_007456911.1) | NM |
Mitogen-activated protein kinase 3(ERK) | Isoform_43270 Isoform_52694 Isoform_78038 | 2.06–23.34 | NM NM NM | 98.87 (XP_007452842.1) 100.00 (XP_007452842.1) 100.00 (XP_007452842.1) | NM NM NM |
Mitogen-activated protein kinase 9 (MAPK9) (JNK) | Isoform_51119 Isoform_55328 | 0.43–1.36 | 100.00 (XP_023972057.1) 99.57 (XP_023972058.1) | 99.59 (XP_007465571.1) 99.13 (XP_007465571.1) | NM NM |
Mitogen-activated protein kinase 8 (MAPK8) (JNK) | Isoform_76485 | 0.05 | NM | 98.82 (XP_007446292.1) | NM |
P38 MAP kinase 11 (P38 β) P38 MAP kinase 12 (P38 γ) P38 MAP kinase 13 (P38 δ) | Isoform_54378 Isoform_28186 Isoform_36890 Isoform_46157 Isoform_9786 Isoform_5589 Isoform_11611 Isoform_12832 Isoform_13409 | 1.77 0.36–3.83 0.06–20.27 | 75.34 (XP_023983249.1) 100.00 (XP_028346617.1) 59.13 (XP_028346617.1) 96.18 (XP_028346617.1) 100.00 (XP_023977640.1) 100.00 (XP_023977640.1) 95.60 (XP_023977640.1) 100.00 (XP_023977640.1) 100.00 (XP_023977640.1) | 73.97 (XP_007454143.1) 97.90 (XP_007453950.1) 56.15 (XP_007467328.1) 94.24 (XP_007453950.1) 96.06 (XP_007467328.1) 96.17 (XP_007467328.1) 93.41 (XP_007467328.1) 96.06 (XP_007467328.1) 94.17 (XP_007467328.1) | NM 98.51 (XP_033721676.1) 56.92 (XP_019805222.1) 94.96 (XP_033721674.1) 95.07 (XP_004313866.1) 95.08 (XP_004313866.1) 92.31 (XP_004313866.1) 95.07 (XP_004313866.1) 95.15 (XP_019805222.1) |
Mitochondrial antiviral-signaling protein (MAVS) | Isoform_11457 Isoform_8429 | 0.19–1.83 | NM NM | 94.08 (XP_007454896.1) 94.08 (XP_007454896.1) | 92.91 (XP_033695234.1) 92.01 (XP_033695233.1) |
TAK1-binding protein 3 (TAB3) | Isoform_24688 | 0.99 | 99.81 (XP_023972426.1) | 98.85 (XP_007456911.1) | NM |
Inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKKe) | Isoform_49506 Isoform_42897 Isoform_44117 Isoform_39392 Isoform_73428 | 0.51–1.29 | NM NM NM NM 100.00 (XP_028342232.1) | 78.84 (XP_007470765.1) 95.02 (XP_007470765.1) 93.63 (XP_007470765.1) 94.96 (XP_007470765.1) 94.32 (XP_007470765.1) | NM NM NM NM NM |
TRAF family member-associated NF-kappa-B activator (TANK) | Isoform_44877 Isoform_30925 Isoform_67916 Isoform_35515 | 0.03–1.95 | NM 98.86 (XP_007107800.2) 100.00 (XP_028334198.1) 100.00 (XP_028334197.1) | 96.77 (XP_019778469.1) 96.80 (XP_019778470.1) 96.77 (XP_007457066.1) 95.12 (XP_007457065.1) | NM 94.65 (XP_019778476.1) 97.42 (XP_019778476.1) 95.89 (XP_019778469.1) |
Interferon regulatory factor 3 (IRF3) | Isoform_25349 Isoform_45963 Isoform_65550 Isoform_73641 Isoform_51357 | 0.6–3.42 | 93.54 (XP_007112499.1) 100.00 (XP_007112499.1) 100.00 (XP_007112499.1) 95.52 (XP_007112501.1) 100.00 (XP_007112498.1) | 87.76 (XP_007463434.1) 94.78 (XP_007463434.1) 95.08 (XP_007463433.1) 96.22 (XP_007463435.1) 95.93 (XP_007463434.1) | 87.41 (XP_033701337.1) NM95.04 (XP_033701337.1) 84.82 (XP_033701337.1) 95.69 (XP_033701337.1) |
Interferon regulatory factor 7 (IRF7) Inhibitor of nuclear factor kappa-B kinase subunit γ (NEMO) C–C motif chemokine 5 (CCL5/RANTES) TNF receptor-associated factor 3 (TRAF3) | Isoform_16065 Isoform_57550 Isoform_32564 Isoform_44904 Isoform_30772 Isoform_32236 Isoform_33819 Isoform_86381 Isoform_14574 | 0.4–1.62 0.13–2.14 0.85 0.1 | 100.00 (XP_028341713.1) 87.47 (XP_028341711.1) 87.47 (XP_028341711.1) 100.00 (XP_028341713.1) NM NM NM 100.00 (XP_028355421.1) NM | 95.04 (XP_007465980.1) 84.88 (XP_007465980.1) 93.44 (XP_007465980.1) 86.14 (XP_007465980.1) 92.79 (XP_007457510.1) 93.45 (XP_007457510.1) 93.45 (XP_007457510.1) 96.83 (XP_007447107.1) 93.04 (XP_007455372.1) | 96.17 (XP_033717457.1) NM95.29 (XP_033717454.1) 95.32 (XP_033717457.1) 92.48 (XP_033705598.1) 93.45 (XP_033705598.1) 93.45 (XP_033705598.1) 95.24 (XP_004322904.1) 94.39 (XP_019776547.2) |
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Sample | Read of Insert | Total Transcripts | Mean Length (bp) | N50 (bp) |
---|---|---|---|---|
Total | 1,056,247 | 96,350 | 1705 | 1996 |
Sequence Size (bp) | UniGene Number |
---|---|
200–500 | 16,252 |
500–1000 | 7251 |
1000–2000 | 6444 |
2000–3000 | 3192 |
≥3000 | 2843 |
Total | 35,982 |
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Wang, D.; Li, Y.; Aierken, R.; Kang, Q.; Wang, X.; Zeng, Q.; Fan, Z.; Zhen, Y.; Zhao, L. Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (Physeter macrocephalus). Genes 2021, 12, 233. https://doi.org/10.3390/genes12020233
Wang D, Li Y, Aierken R, Kang Q, Wang X, Zeng Q, Fan Z, Zhen Y, Zhao L. Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (Physeter macrocephalus). Genes. 2021; 12(2):233. https://doi.org/10.3390/genes12020233
Chicago/Turabian StyleWang, Daling, Ying Li, Reyilamu Aierken, Qi Kang, Xianyan Wang, Qianhui Zeng, Zhichang Fan, Yu Zhen, and Liyuan Zhao. 2021. "Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (Physeter macrocephalus)" Genes 12, no. 2: 233. https://doi.org/10.3390/genes12020233
APA StyleWang, D., Li, Y., Aierken, R., Kang, Q., Wang, X., Zeng, Q., Fan, Z., Zhen, Y., & Zhao, L. (2021). Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (Physeter macrocephalus). Genes, 12(2), 233. https://doi.org/10.3390/genes12020233