De novo transcriptomic analysis of gonad of Strongylocentrotus nudus and gene discovery for biosynthesis of polyunsaturated fatty acids

다국어 초록 (Multilingual Abstract)

Background Strongylocentrotus nudus is an important cultured sea urchin species in north China, because its gonad is rich in unsaturated fatty acids, particularly long polyunsaturated fatty acids (LC-PUFAs). These PUFAs play pleiotropic and crucial roles in a wide range of biological process.
Objective However, the genes contributing to biosynthesis PUFAs have not been elucidated yet, and the molecular mechanism relative to the difference in PUFA composition between male and female gonad as been revealed but the corresponding has not been understood.
Methods In this paper, solexa sequencing based transcriptomic approach was used to identify and characterize the key genes relative to PUFA synthesis and further conducted different expressed genes between male and female gonad.
Results A total of 130,124 transcripts and 189330 unigenes were de novo assembled from 64.32 Gb data. Next, these unigenes were subjected to functional annotation by mapping to six public databases, and this process revealed a lot of genes involving in lipid metabolism. In addition, three types of fatty acids front-end desaturase and three species of very long fatty acids elongase were identified and the pathway for PUFA biosynthesis was hypothesized. Last, comparative analysis revealed the higher expression level of Δ5 desaturase, Δ6 desaturase, ELOVL-4, -6 and -7 in male gonad compared with female.
Conclusion This results could plausible explain the differ in composition of PUFAs between male and female gonad of sea urchin.

참고문헌 (Reference)

1 Ye J, "WEGO: a web tool for plotting GO annotations" 34 (34): W293-W297, 2006

2 Nicole M White, "Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer" Springer Science and Business Media LLC 15 (15): 2014

3 Rui Hou, "Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX" Public Library of Science (PLoS) 6 (6): e21560-, 2011

4 Huixia Du, "Transcriptome Sequencing and Characterization for the Sea Cucumber Apostichopus japonicus (Selenka, 1867)" Public Library of Science (PLoS) 7 (7): e33311-, 2012

5 Shubo Jin, "Transcriptome Analysis of Androgenic Gland for Discovery of Novel Genes from the Oriental River Prawn, Macrobrachium nipponense, Using Illumina Hiseq 2000" Public Library of Science (PLoS) 8 (8): e76840-, 2013

6 Alicia Oshlack, "Transcript length bias in RNA-seq data confounds systems biology" Springer Science and Business Media LLC 4 (4): 14-, 2009

7 Hashimoto K, "The repertoire of desaturases and elongases reveals fatty acid variations in 56eukaryotic genomes" 49 (49): 183-191, 2008

8 Houk MS, "The formation and early differentiation of sea urchin gonads" 159 (159): 280-294, 1980

9 Meesapyodsuk D, "The Front-end desaturase : structure, function, evolution and biotechnological use" 47 (47): 227-237, 2012

10 Tong SY, "Study on lipid and fatty acids composition of three kinds of Echinoidea’s gonad" 22 (22): 247-252, 1998

11 Eli Meyer, "Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx" Springer Science and Business Media LLC 10 (10): 219-, 2009

12 Dodge CA, "Seasonal variation in the effects of food availability on gametogenesis in the purple urchin(Strongylocentrotus purpuratus)" 159 (159): 427-433, 2012

13 Pennisi E, "Sea urchin genome confirms kinship to humans and other vertebrates" 314 (314): 908-909, 2006

14 Rogowski MP, "SCD1 activity in muscle increases triglyceride PUFA content, exercise capacity, and PPARδ expression in mice" 54 (54): 2636-2646, 2013

15 Marioni JC, "RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays" 18 (18): 1509-1517, 2008

16 Unuma T, "Quantitative changes in yolk protein and other components in the ovary and testis of the sea urchin Pseudocentrotus depressus" 206 (206): 365-372, 2003

17 Lei Sun, "Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study" Springer Science and Business Media LLC 13 (13): 331-, 2012

18 Wathes DC, "Polyunsaturated fatty acids in male and female reproduction" 77 : 190-201, 2007

19 Bazinet RP, "Polyunsaturated fatty acids and their metabolites in brain function and disease" 15 : 771-785, 2014

20 Della Sala G, "Polyketide genes in the marine sponge Plakortis simplex : a new group of monomodular type I polyketide synthases from sponge symbionts" 5 (5): 809-818, 2013

21 Liu H, "PUFA biosynthesis pathway in marine Scallop Chlamys nobilis Reeve" 62 (62): 12384-12391, 2014

22 Barnathan G, "Non-methylene-interrupted fatty acids from marine invertebrates : Occurrence, characterization and biological properties" 91 (91): 671-678, 2009

23 Monroig O, "Multiple genes for functional 6 fatty acyl desaturases (Fad) in Atlantic salmon (Salmo salar L.): gene and cDNA characterization, functional expression, tissue distribution and nutritional regulation" 1801 (1801): 1072-1081, 2010

24 Bulgakov AA, "Mannanbinding lectin of the sea urchin Strongylocentrotus nudus" 15 (15): 73-86, 2013

25 Martínez-Pita I, "Males and females gonad fatty acids of the sea urchins Paracentrotus lividus and Arbacia lixula (Echinodermata)" 64 : 135-142, 2010

26 Tamura K, "MEGA6: Molecular evolutionary genetics analysis version 6.0" 30 : 2725-2729, 2013

27 Zhukova NV, "Lipids and fatty acids of Nudibranch Mollusks:Potential sources of bioactive compounds" 12 (12): 4578-4592, 2014

28 Djebali S, "Landscape of transcription in human cells" 489 (489): 101-108, 2012

29 Qiong Lin, "Involvement of CitCHX and CitDIC in Developmental-Related and Postharvest-Hot-Air Driven Citrate Degradation in Citrus Fruits" Public Library of Science (PLoS) 10 (10): e0119410-, 2015

30 Goel M, "Intermediary metabolism in sea urchin: the first inferences from the genome sequence" 300 (300): 282-292, 2006

31 Wu K, "Identification, expression analysis, and the regulating function on C/EBPs of KLF10 in Dalian purple sea urchin, Strongylocentrotus nudus" 60 (60): 837-849, 2017

32 Jakhesara SJ, "Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus" 165 (165): 37-44, 2013

33 Coline Billerey, "Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing" Springer Science and Business Media LLC 15 (15): 499-, 2014

34 Monroig O, "Identification of a Δ5-like fatty acyl desaturase from the cephalopod Octopus vulgaris (Cuvier 1797) involved in the biosynthesis of essential fatty acids" 14 (14): 411-422, 2012

35 Lands B, "Historical perspectives on the impact of n-3 and n-6nutrients on health" 55 : 17-29, 2014

36 Siriwardhana N, "Health benefits of n-3 polyunsaturated fatty acids : eicosapentaenoic acid and docosahexaenoic acid" 65 : 211-222, 2012

37 Liu H, "Functional characterization of a Δ5-like fatty acyl desaturase and its expression during early embryogenesis in the noble scallop Chlamys nobilis Reeve" 41 (41): 7437-7445, 2014

38 Luís Filipe Costa Castro, "Functional Desaturase Fads1 (Δ5) and Fads2 (Δ6) Orthologues Evolved before the Origin of Jawed Vertebrates" Public Library of Science (PLoS) 7 (7): e31950-, 2012

39 Grabherr MG, "Full-length transcriptome assembly from RNA-seq data without a reference genome" 29 (29): 644-652, 2011

40 Kelly JR, "Fatty acid profiles in the gonads of the sea urchin Strongylocentrotus droebachiensis on natural algal diets" 373 : 1-9, 2008

41 Carboni S, "Fatty acid profiles during gametogenesis in sea urchin (Paracentrotus lividus): effects of dietary inputs on gonad, egg and embryo profiles" 164 (164): 376-382, 2013

42 Purdy JG, "Fatty acid elongase 7 catalyzes lipidome remodeling essential for human cytomegalovirus replication" 10 (10): 1375-1385, 2015

43 Itabashi Y, "Fatty acid composition of the gonad of the sea urchin Strongylocentrotus nudus fed Fish" 47 (47): 703-707, 1998

44 Zhu BW, "Extraction of lipid from sea urchin (Strongylocentrotus nudus) gonad by enzyme-assisted aqueous and supercritical carbon dioxide methods" 230 (230): 737-743, 2010

45 Beeble A, "Expression pattern of polyketide synthase-2 during sea urchin development" 12 (12): 7-10, 2012

46 IE Makarenko, "Effects of lipid extract of sea urchins gonads in metabolic syndrome animal model" Georg Thieme Verlag KG 79 (79): 2013

47 Martínez I, "Echinoderm research 2001" Swets and Zeitlinger 2003

48 Fonseca-Madrigal J, "Diversification of substrate specificities in teleostei Fads2 : characterization of Δ4 and Δ6Δ5 desaturases of Chirostoma estor" 55 (55): 1408-1419, 2014

49 Puig-Oliveras A, "Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition" 9 (9): e99720-, 2014

50 Kornprobst JM, "Demospongic acids revisited" 8 (8): 2569-2577, 2010

51 Tosi F, "Delta-5 and delta-6 desaturases:crucial enzymes in polyunsaturated fatty acid-related pathways with pleiotropic influences in health and disease" 824 : 61-81, 2014

52 Raymond WW, "Degradation state of algal diets affects fatty acid composition but not size of red urchin gonads" 509 : 213-225, 2014

53 Thomas Holder, "Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability" Springer Science and Business Media LLC 8 (8): 2013

54 Li-xin Xiang, "Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish" Springer Science and Business Media LLC 11 (11): 472-, 2010

55 Haas BJ, "De novo transcript sequence reconstruction from RNA-Seq : reference generation and analysis with Trinity" 8 (8): 1494-1512, 2013

56 Dejun Li, "De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)" Springer Science and Business Media LLC 13 (13): 192-, 2012

57 Ding J, "Comparative studies on urchin in gonad fatty acid composition and β-carotene content in north china sea section" 13 (13): 122-128, 2011

58 Larkin MA, "Clustal W and Clustal X version 2.0" 23 (23): 2947-2948, 2007

59 Li M, "Characterization of two Δ5 fatty acyl desaturases in abalone (Haliotis discus hannai Ino)" 416 : 48-56, 2013

60 Feng LF, "Changes in lipid characteristics and fatty acid contents of developmental yolk-sac larvae of Epinephelus awoara and Trachinotus ovatus" 21 (21): 720-727, 2012

61 Conesa A, "Blast2GO : a universal tool for annotation, visualization and analysis in functional genomics research" 21 (21): 3674-3676, 2005

62 Monroig Ó, "Biosynthesis of polyunsaturated fatty acids in marine invertebrates: recent advances in molecular mechanisms" 11 (11): 3998-4018, 2013

63 Uttaro AD, "Biosynthesis of polyunsaturated fatty acids in lower eukaryotes" 58 (58): 563-571, 2006

64 Bell MV, "Biosynthesis of eicosapentaenoic acid in the sea urchin Psammechinus miliaris" 36 (36): 79-82, 2001

65 Raymond JF, "Biochemical content, energy composition and reproductive effort in the broadcasting sea star Asterias vulgaris over the spawning period" 341 : 32-44, 2007

66 Naganuma T, "Biochemical characterization of the very long-chain fatty acid elongase ELOVL7" 585 : 3337-3341, 2011

67 Monroig O, "Avances en Nutrición Acuícola XI-Memorias del Décimo Primer Simposio Internacional de Nutrición Acuícola" Universidad Autónoma de Nuevo León 2011

68 Jordi Corominas, "Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition" Springer Science and Business Media LLC 14 (14): 843-, 2013

69 Bookbinder LH, "Anaerobic and aerobic energy metabolism in ovaries of the sea urchin Strongylocentrotus droebachiensis" 93 (93): 103-110, 1986

70 Castoe TA, "A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs" 392 (392): 47-58, 2007

71 Warren R Francis, "A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly" Springer Science and Business Media LLC 14 (14): 167-, 2013