Next-generation Transcriptome Assembly

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2011 Sep 8

PMID 21897427

Citations 553

Authors

Jeffrey A Martin

Zhong Wang

Affiliations

Soon will be listed here.

Abstract

Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.

Citing Articles

Chromosome number variation and phylogenetic divergence of East Asian Cirsium sect. Onotrophe subsect. Nipponocirsium (Compositae), with a new species from Taiwan.

Chang C, Liao P, Tzeng H, Kusumi J, Su Z, Tseng Y Bot Stud. 2025; 66(1):8.

PMID: 39953173 PMC: 11828781. DOI: 10.1186/s40529-025-00454-2.

Unveiling the dual role of biocolonization: a case study on the deterioration and preservation of sandstone monuments in Leshan Giant Buddha, China.

Zhu C, Wang B, Liu Z, Guo Y, Zheng L, Zhang B World J Microbiol Biotechnol. 2025; 41(2):25.

PMID: 39762472 DOI: 10.1007/s11274-024-04237-y.

Primes a Multilayered Transcriptional Defense Response to the Nematode spp. in Tomato.

Gonzalez-Cardona C, Lopez W, Jovel J, Soto-Suarez M, Ceballos-Aguirre N Int J Mol Sci. 2024; 25(23).

PMID: 39684296 PMC: 11641443. DOI: 10.3390/ijms252312584.

Pavlovian-Type Learning in Environmental Bacteria: Regulation of Herbicide Resistance by Arsenic in Pseudomonas putida.

Paez-Espino D, Durante-Rodriguez G, Fernandes E, Carmona M, de Lorenzo V Environ Microbiol. 2024; 26(12):e70012.

PMID: 39667752 PMC: 11637737. DOI: 10.1111/1462-2920.70012.

Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets.

Sergio Alberto G, Maximo R, Andres R, Sergio L, Norma P Bioinform Biol Insights. 2024; 18:11779322241274957.

PMID: 39649541 PMC: 11622296. DOI: 10.1177/11779322241274957.

References

Dalloul R, Long J, Zimin A, Aslam L, Beal K, Blomberg L . Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 2010; 8(9). PMC: 2935454. DOI: 10.1371/journal.pbio.1000475. View

Fukuda Y, Washio T, Tomita M . Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Nucleic Acids Res. 1999; 27(8):1847-53. PMC: 148392. DOI: 10.1093/nar/27.8.1847. View

Greninger A, Chen E, Sittler T, Scheinerman A, Roubinian N, Yu G . A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One. 2010; 5(10):e13381. PMC: 2956640. DOI: 10.1371/journal.pone.0013381. View

Burset M, Seledtsov I, Solovyev V . Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res. 2000; 28(21):4364-75. PMC: 113136. DOI: 10.1093/nar/28.21.4364. View

Wilhelm B, Landry J . RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods. 2009; 48(3):249-57. DOI: 10.1016/j.ymeth.2009.03.016. View

Katz Y, Wang E, Airoldi E, Burge C . Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods. 2010; 7(12):1009-15. PMC: 3037023. DOI: 10.1038/nmeth.1528. View

Birol I, Jackman S, Nielsen C, Qian J, Varhol R, Stazyk G . De novo transcriptome assembly with ABySS. Bioinformatics. 2009; 25(21):2872-7. DOI: 10.1093/bioinformatics/btp367. View

Taylor R . An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics. 2011; 11 Suppl 12:S1. PMC: 3040523. DOI: 10.1186/1471-2105-11-S12-S1. View

Kozarewa I, Ning Z, Quail M, Sanders M, Berriman M, Turner D . Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods. 2009; 6(4):291-5. PMC: 2664327. DOI: 10.1038/nmeth.1311. View

10.

Mizuno H, Kawahara Y, Sakai H, Kanamori H, Wakimoto H, Yamagata H . Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics. 2010; 11:683. PMC: 3016417. DOI: 10.1186/1471-2164-11-683. View

11.

Butler J, MacCallum I, Kleber M, Shlyakhter I, Belmonte M, Lander E . ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 2008; 18(5):810-20. PMC: 2336810. DOI: 10.1101/gr.7337908. View

12.

Rodrigue S, Materna A, Timberlake S, Blackburn M, Malmstrom R, Alm E . Unlocking short read sequencing for metagenomics. PLoS One. 2010; 5(7):e11840. PMC: 2911387. DOI: 10.1371/journal.pone.0011840. View

13.

Levin J, Yassour M, Adiconis X, Nusbaum C, Thompson D, Friedman N . Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 2010; 7(9):709-15. PMC: 3005310. DOI: 10.1038/nmeth.1491. View

14.

Kinsella M, Harismendy O, Nakano M, Frazer K, Bafna V . Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011; 27(8):1068-75. PMC: 3072550. DOI: 10.1093/bioinformatics/btr085. View

15.

Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman S . De novo assembly and analysis of RNA-seq data. Nat Methods. 2010; 7(11):909-12. DOI: 10.1038/nmeth.1517. View

16.

Ozsolak F, Ting D, Wittner B, Brannigan B, Paul S, Bardeesy N . Amplification-free digital gene expression profiling from minute cell quantities. Nat Methods. 2010; 7(8):619-21. PMC: 2975601. DOI: 10.1038/nmeth.1480. View

17.

Perkins T, Kingsley R, Fookes M, Gardner P, James K, Yu L . A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet. 2009; 5(7):e1000569. PMC: 2704369. DOI: 10.1371/journal.pgen.1000569. View

18.

Paszkiewicz K, Studholme D . De novo assembly of short sequence reads. Brief Bioinform. 2010; 11(5):457-72. DOI: 10.1093/bib/bbq020. View

19.

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

20.

Metzker M . Sequencing technologies - the next generation. Nat Rev Genet. 2009; 11(1):31-46. DOI: 10.1038/nrg2626. View