Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Vidotto, Michele ^a   Grapputo, Alessandro ^a   Boscari, Elisa ^a   Barbisan, Federica ^a   Coppe, Alessandro ^a   Grandi, Gilberto ^b   Kumar, Abhishek ^a,c   Congiu, Leonardo ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF FERRARA   (Italy)

^c UNIVERSITY OF KIEL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ADRIATIC STURGEON; AMINO ACID SEQUENCE; ARTICLE; BRAIN; DNA LIBRARY; ENDANGERED SPECIES; EXPRESSED SEQUENCE TAG; FEMALE; GENETIC ANALYSIS; GENETIC SCREENING; GONAD; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; SEX DETERMINATION; SINGLE NUCLEOTIDE POLYMORPHISM; STURGEON;

ANIMALS; DATABASES, PROTEIN; ENDANGERED SPECIES; EVOLUTION, MOLECULAR; FEMALE; FISHES; GENE EXPRESSION PROFILING; MALE; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; NUCLEOTIDES; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, UNTRANSLATED; SEQUENCE ANALYSIS; SEX DETERMINATION PROCESSES;

ACIPENSER NACCARII; ACIPENSERIDAE; ANIMALIA;

EID: 84879057753     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-407     Document Type: Article

References (56)

1. Congiu L, Pujolar JM, Forlani A, Cenadelli S, Dupanloup I, Barbisan F, Galli A, Fontana F. Managing polyploidy in ex situ conservation genetics: the case of the critically endangered Adriatic sturgeon (Acipenser naccarii). PLoS One 2011, 6:e18249. 10.1371/journal.pone.0018249, 3066226, 21483472.
2. Bemis WE, Findeis EK, Grande L. An overview of Acipenseriformes. Environ Biol Fishes 1997, 48:25-71.
3. Ludwig A, Belfiore NM, Pitra C, Svirsky V, Jenneckens I. Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus). Genetics 2001, 158:1203-1215. 1461728, 11454768.
4. Fontana F, Congiu L, Mudrak VA, Quattro JM, Smith TIJ, Ware K, Doroshov SI. Evidence of hexaploid karyotype in shortnose sturgeon. Genome 2008, 51:113-119. 10.1139/G07-112, 18356945.
5. Boscari E, Barbisan F, Congiu L. Inheritance pattern of microsatellite loci in the polyploid Adriatic sturgeon (Acipenser naccarii). Aquaculture 2011, 321:223-229.
6. Fontana F, Lanfredi M, Kirschbaum F, Garrido-Ramos MA, Robles F, Forlani A, Congiu L. Comparison of karyotypes of Acipenser oxyrinchus and A. sturio by chromosome banding and fluorescent in situ hybridization. Genetica 2008, 132:281-286. 10.1007/s10709-007-9171-4, 17624498.
7. Birstein VJ, Vasiliev VP. Tetraploid-octoploid relationships and karyological evolution in the order Acipenseriformes (Pisces) karyotypes, nucleoli, and nucleolus-organizer regions in four acipenserid species. Genetica 1987, 72:3-12.
8. Fontana F, Lanfredi M, Chicca M, Congiu L, Tagliavini J, Rossi R. Fluorescent in situ hybridization with rDNA probes on chromosomes of Acipenser ruthenus and Acipenser naccarii (Osteichthyes Acipenseriformes). Genome 1999, 42:1008-1012.
9. Peng H, Zhang J, Wu X. The ploidy effects in plant gene expression: Progress, problems and prospects. Sci China C Life Sci 2008, 51:295-301. 10.1007/s11427-008-0039-3, 18368306.
10. Ludwig A. Identification of Acipenseriformes species in trade. J Appl Ichthyol 2008, 24:2-19.
11. Wuertz S, Gaillard S, Barbisan F, Carle S, Congiu L, Forlani A, Aubert J, Kirschbaum F, Tosi E, Zane L, Grillasca J-P. Extensive screening of sturgeon genomes by random screening techniques revealed no sex-specific marker. Aquaculture 2006, 258:685-688.
12. Van Eenennaam AL, Van Eenennaam JP, Medrano JF, Doroshov SI. Evidence of female heterogametic genetic sex determination in white sturgeon. J Hered 1999, 90:231-233.
13. Keyvanshokooh S, Pourkazemi M, Kalbassi MR. The RAPD technique failed to identify sex-specific sequences in beluga (Huso huso). J Appl Ichthyol 2007, 23:1-2.
14. FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, FastQC.
15. Sato Y, Nishida M. Teleost fish with specific genome duplication as unique models of vertebrate evolution. Environ Biol Fishes 2010, 88:169-188.
16. Krieger J, Fuerst PA. Evidence for a slowed rate of molecular evolution in the order acipenseriformes. Mol Biol Evol 2002, 19:891-897. 10.1093/oxfordjournals.molbev.a004146, 12032245.
17. Woods IG. The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res 2005, 15:1307-1314. 10.1101/gr.4134305, 1199546, 16109975.
18. Pang KC, Frith MC, Mattick JS. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 2006, 22:1-5. 10.1016/j.tig.2005.10.003, 16290135.
19. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009, 25:1335-1337. 10.1093/bioinformatics/btp157, 2732312, 19307242.
20. Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber APM. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics 2011, 12:227. 10.1186/1471-2164-12-227, 3224338, 21569327.
21. Chao A. Estimating Population Size for Sparse Data in Capture-Recapture Experiments. Biometrics 1989, 45:427-438.
22. Schwartz TS, Tae H, Yang Y, Mockaitis K, Van Hemert JL, Proulx SR, Choi J-H, Bronikowski AM. A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics 2010, 11:694. 10.1186/1471-2164-11-694, 3014983, 21138572.
23. Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009, 5:e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
24. Hale MC, Jackson JR, DeWoody JA. Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens). Genetica 2010, 138:745-756. 10.1007/s10709-010-9455-y, 20386959.
25. Grandi G, Chicca M. Histological and ultrastructural investigation of early gonad development and sex differentiation in Adriatic sturgeon (Acipenser naccarii, Acipenseriformes, Chondrostei). J Morphol 2008, 269:1238-1262. 10.1002/jmor.10657, 18636535.
26. Amberg JJ, Goforth R, Stefanavage T, Sepúlveda MS. Sexually dimorphic gene expression in the gonad and liver of shovelnose sturgeon (Scaphirhynchus platorynchus). Fish Physiol Biochem 2009, 36:923-932.
27. Berbejillo J, Martinez-Bengochea A, Bedó G, Vizziano-Cantonnet D. Expression of dmrt1 and sox9 during gonadal development in the Siberian sturgeon (Acipenser baerii). Fish Physiol Biochem 2013, 39:91-94. 10.1007/s10695-012-9666-5, 22688449.
28. Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, Jindo T, Kobayashi D, Shimada A, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Morishita S, Kohara Y. The medaka draft genome and insights into vertebrate genome evolution. Nature 2007, 447:714-719. 10.1038/nature05846, 17554307.
29. Ferguson-Smith M. The Evolution of Sex Chromosomes and Sex Determination in Vertebrates and the Key Role of DMRT1. Sex Dev 2007, 1:2-11. 10.1159/000096234, 18391511.
30. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120. 10.1007/BF01731581, 7463489.
31. Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA. Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res 2004, 32:e37. 10.1093/nar/gnh031, 373426, 14973331.
32. Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG. Next generation transcriptomes for next generation genomes using est2assembly. BMC Bioinforma 10:447-447.
33. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S. Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. Genome Res 2004, 14:1147-1159. 10.1101/gr.1917404, 419793, 15140833.
34. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008, 17:1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
35. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11:1725-1729. 10.1101/gr.194201, 311141, 11591649.
36. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
37. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
38. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinforma 2009, 10:421.
39. Cao H, Leng X, Li C, Wei Q, Gui J, Cheng H, Zhou R. EST dataset of pituitary and identification of somatolactin and novel genes in Chinese sturgeon, Acipenser sinensis. Mol Biol Rep 2012, 39:4647-4653. 10.1007/s11033-011-1256-6, 21986641.
40. Lazzari B, Mariani V, Malinverni R, Caprera A, Giuffra E. A comparative gene index for the white sturgeon Acipenser transmontanus. Mar Genomics 2008, 1:15-21. 10.1016/j.margen.2008.04.002, 21798149.
41. Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC. Integrative analysis of environmental sequences using MEGAN4. Genome Res 2011, 21:1552-1560. 10.1101/gr.120618.111, 3166839, 21690186.
42. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008, 36:3420-3435. 10.1093/nar/gkn176, 2425479, 18445632.
43. Ewing B, Green P. Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet 2000, 25:232-234. 10.1038/76115, 10835644.
44. Baillargeon S, Rivest L-P. Rcapture: Loglinear Models for Capture-Recapture in R. J. Stat. Softw 2007, 19:1-31. 3074178, 21494410.
45. Bobrowicz AJ, Lightowlers RN, Chrzanowska-Lightowlers Z. Polyadenylation and degradation of mRNA in mammalian mitochondria: a missing link?. Biochem Soc Trans 2008, 36:517-519. 10.1042/BST0360517, 18481994.
46. Rorbach J, Minczuk M. The post-transcriptional life of mammalian mitochondrial RNA. Biochem J 2012, 444:357-373. 10.1042/BJ20112208, 22642575.
47. Pala I, Schartl M, Thorsteinsdóttir S, Coelho MM. Sex Determination in the Squalius alburnoides Complex: An Initial Characterization of Sex Cascade Elements in the Context of a Hybrid Polyploid Genome. PLoS One 2009, 4:e6401. 10.1371/journal.pone.0006401, 2713423, 19636439.
48. Shirak A, Seroussi E, Cnaani A, Howe AE, Domokhovsky R, Zilberman N, Kocher TD, Hulata G, Ron M. Amh and Dmrta2 Genes Map to Tilapia (Oreochromis spp.) Linkage Group 23 Within Quantitative Trait Locus Regions for Sex Determination. Genetics 2006, 174:1573-1581. 10.1534/genetics.106.059030, 1667067, 16951079.
49. McClelland K, Bowles J, Koopman P. Male sex determination: insights into molecular mechanisms. Asian J Androl 2012, 14:164-171. 10.1038/aja.2011.169, 22179516.
50. Katoh K, Frith MC. Adding unaligned sequences into an existing alignment using MAFFT and LAST. Bioinformatics 2012, 28:3144-3146. 10.1093/bioinformatics/bts578, 3516148, 23023983.
51. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Res 2009, 38:D211-D222. 2808889, 19920124.
52. Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011, 12:443-451. 10.1038/nrg2986, 3593722, 21587300.
53. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. Arxiv E-Prints 2012, 1207:3907.
54. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008, 18:763-770. 10.1101/gr.070227.107, 2336812, 18212088.
55. MISA - MIcroSAtellite identification tool http://pgrc.ipk-gatersleben.de/misa/.
56. Mudunuri SB, Rao AA, Pallamsetty S, Nagarajaram HA. Comparative analysis of microsatellite detecting software: a significant variation in results and influence of parameters. Proc. Int. Symp. Biocomput 2010, 38:1-38:7. New York, NY, USA: ACM.