不同组装软件在系统发育基因组学中的应用比较

doi:10.3969/j.issn.1000-1565.2023.02.009

摘要/Abstract

摘要： 为了筛选出最适合于超级保守元件(ultra-conserved elements,UCE)序列组装的软件,分别使用5款组装软件SPAdes、ABySS、Velvet、Trinity和Minia对17个UCE捕获测序文库进行组装.结果发现:5款组装软件对UCE数据的组装结果不同,Trinity组装所耗时间明显比其他软件长;SPAdes和Trinity的组装结果较好,得到的可观长度的重叠群(contigs)总数较多,产生的长片段(>250 bp)contigs较其他3款软件更多,但是SPAdes捕获到的UCE数量最多,因此,相比于其他4款组装软件,SPAdes更适合UCE数据的组装. 本研究为基于UCE的系统发育基因组学分析提供了参考.

关键词: 数据分析, 超级保守元件, 系统发育基因组学

Abstract: To select the most suitable assembler for ultra-conserved elements(UCE)phylogenomic practice, five different assembly softwares, SPAdes, ABySS, Velvet, Trinity and Minia were applied, to assemble 17 UCE captured sequencing libraries, respectively. The results showed that among the five assemblers, Trinity consumed significantly longer computational time than the others; SPAdes and Trinity both assembled more contigs and obtained more longer contigs(> 250 bp)than the other three assemblers, but SPAdes captured the highest number of UCE loci. Therefore, SPAdes is more suitable for the assembly of UCE data than the other assembly softwares. This study provides a technical reference for the practice of UCE-based phylogenomic studies.

Key words: data analysis, UCE, phylogenomics

中图分类号:

Q951

王耀卓,张文强,张俊霞. 不同组装软件在系统发育基因组学中的应用比较[J]. 河北大学学报(自然科学版), 2023, 43(2): 171-178.

WANG Yaozhuo, ZHANG Wenqiang, ZHANG Junxia. Comparison of application of assemblers in phylogenomics[J]. Journal of Hebei University(Natural Science Edition), 2023, 43(2): 171-178.

参考文献

[1] YOUNG A D, GILLUNG J P. Phylogenomics — principles, opportunities and pitfalls of big-data phylogenetics[J]. Syst Entomol, 2020, 45(2): 225-247. DOI: 10.1111/syen.12406.
[2] ZHANG J, LAI J. Phylogenomic approaches in systematic studies[J]. Zool Syst, 2020, 45(3): 151-162. DOI:10.11865/zs.202021.
[3] PRUM R O, BERV J S, DORNBURG A, et al. A comprehensive phylogeny of birds(Aves)using targeted next-generation DNA sequencing[J]. Nature, 2015, 526(7574): 569-573. DOI:10.1038/nature15697.
[4] WALKER J F, BROWN J W, SMITH S A. Analyzing contentious relationships and outlier genes in phylogenomics[J]. Syst Biol, 2018, 67(5): 916-924. DOI:10.1093/sysbio/syy043.
[5] CHEN M Y, LIANG D, ZHANG P. Phylogenomic resolution of the phylogeny of laurasiatherian mammals: exploring phylogenetic signals within coding and noncoding sequences[J]. Genome Biol Evol, 2017, 9(8): 1998-2012. DOI:10.1093/gbe/evx147.
[6] GARRISON N L, RODRIGUEZ J, AGNARSSON I, et al. Spider phylogenomics: untangling the spider tree of life[J]. PeerJ, 2016, 4(2): e1719. DOI:10.7717/peerj.1719.
[7] MADDISON W P, EVANS S C, HAMILTON C A, et al. A genome-wide phylogeny of jumping spiders(Araneae, Salticidae), using anchored hybrid enrichment[J]. Zookeys, 2017, 2017(695): 89-101. DOI:10.3897/zookeys.695.13852.
[8] FORTHMAN M, MILLER C W, KIMBALL R T. Phylogenomic analysis suggests Coreidae and Alydidae(Hemiptera: Heteroptera)are not monophyletic[J]. Zool Scr, 2019, 48(4): 520-534. DOI:10.1111/zsc.12353.
[9] FAIRCLOTH B C, MCCORMACK J E, CRAWFORD N G, et al. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales[J]. Syst Biol, 2012, 61(5): 717-726. DOI:10.1093/sysbio/sys004.
[10] BEJERANO G, PHEASANT M, MAKUNIN I, et al. Ultraconserved elements in the human genome[J]. Science, 2004, 304(5675): 1321-1325. DOI:10.1126/science.1098119.
[11] STEPHEN S, PHEASANT M, MAKUNIN I V, et al. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock[J]. Mol Biol Evol, 2007, 25(2): 402-408. DOI:10.1093/molbev/msm268.
[12] MCCORMACK J E, FAIRCLOTH B C, CRAWFORD N G, et al. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis[J]. Genome Res, 2012, 22(4): 746-754. DOI:10.1101/gr.125864.111.
[13] MCCORMACK J E, HARVEY M G, FAIRCLOTH B C, et al. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing[J]. PLoS One, 2013, 8(1): e54848. DOI:10.1371/journal.pone.0054848.
[14] MEIKLEJOHN K A, FAIRCLOTH B C, GLENN T C, et al. Analysis of a rapid evolutionary radiation using ultraconserved elements: evidence for a bias in some multispecies coalescent methods[J]. Syst Biol, 2016, 65(4): 612-627. DOI:10.1093/sysbio/syw014.
[15] CHEN D, BRAUN E L, FORTHMAN M, et al. A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: placement of the partridge genus Tropicoperdix within the galliformes[J]. Mol Phylogenetics Evol, 2018, 129: 304-314. DOI:10.1016/j.ympev.2018.09.005.
[16] WHITE N D, BRAUN M J. Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds(Strisores)[J]. Mol Phylogenetics Evol, 2019, 141:106611. DOI:10.1016/j.ympev.2019.106611.
[17] FAIRCLOTH B C, SORENSON L, SANTINI F, et al. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements(UCEs)[J]. PLoS One, 2013, 8(6): e65923. DOI:10.1371/journal.pone.0065923.
[18] LONGO S J, FAIRCLOTH B C, MEYER A, et al. Phylogenomic analysis of a rapid radiation of misfit fishes(Syngnathiformes)using ultraconserved elements[J]. Mol Phylogenetics Evol, 2017, 113: 33-48. DOI:10.1016/j.ympev.2017.05.002.
[19] HULSEY C D, ZHENG J, FAIRCLOTH B C, et al. Phylogenomic analysis of Lake Malawi cichlid fishes: further evidence that the three-stage model of diversification does not fit[J]. Mol Phylogenetics Evol, 2017, 114: 40-48. DOI:10.1016/j.ympev.2017.05.027.
[20] OCHOA L E, DATOVO A, DONASCIMIENTO C, et al. Phylogenomic analysis of trichomycterid catfishes(Teleostei: Siluriformes)inferred from ultraconserved elements[J]. Sci Rep, 2020, 10: 2697. DOI:10.1038/s41598-020-59519-w.
[21] PIE M R, BORNSCHEIN M R, RIBEIRO L F, et al. Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest[J]. Mol Phylogenetics Evol, 2019, 141: 106627. DOI:10.1016/j.ympev.2019.106627.
[22] GUILLORY W X, MUELL M R, SUMMERS K, et al. Phylogenomic reconstruction of the neotropical poison frogs(Dendrobatidae)and their conservation[J]. Diversity, 2019, 11(8): 126. DOI:10.3390/d11080126.
[23] FAIRCLOTH B C, BRANSTETTER M G, WHITE N D, et al. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera[J]. Mol Ecol Resour, 2015, 15(3): 489-501. DOI:10.1111/1755-0998.12328.
[24] BRANSTETTER M G, DANFORTH B N, PITTS J P, et al. Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees[J]. Curr Biol, 2017, 27(7): 1019-1025. DOI:10.1016/j.cub.2017.03.027.
[25] CRUAUD A, NIDELET S, ARNAL P, et al. Optimized DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol[J]. Mol Ecol Res, 2019, 19(3): 702-710. DOI:10.1111/1755-0998.13006.
[26] SUN X, DING Y H, ORR M C, et al. Streamlining universal single-copy orthologue and ultraconserved element design: a case study in Collembola[J]. Mol Ecol Resour, 2020, 20(3): 706-717. DOI:10.1111/1755-0998.13146.
[27] STARRETT J, DERKARABETIAN S, HEDIN M, et al. High phylogenetic utility of an ultraconserved element probe set designed for Arachnida[J]. Mol Ecol Resour, 2017, 17(4): 812-823. DOI:10.1111/1755-0998.12621.
[28] HEDIN M, DERKARABETIAN S, ALFARO A, et al. Phylogenomic analysis and revised classification of atypoid mygalomorph spiders(Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci[J]. PeerJ, 2019, 7: e6864. DOI:10.7717/peerj.6864.
[29] DERKARABETIAN S, BENAVIDES L R, GIRIBET G. Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault[J]. Mol Ecol Resour, 2019, 19(6): 1531-1544. DOI:10.1111/1755-0998.13072.
[30] MADDISON W P,MADDISON D R,DERKARABETIAN S, et al. Sitticine jumping spiders: phylogeny,classification, and chromosomes(Araneae, Salticidae, Sitticini)[J]. Zookeys, 2020,925:1-54.DOI: 10.3897/zookeys.925.39691.
[31] FAIRCLOTH B C. PHYLUCE is a software package for the analysis of conserved genomic loci[J]. Bioinformatics, 2015, 32(5): 786-788. DOI:10.1093/bioinformatics/btv646.
[32] PRJIBELSKI A, ANTIPOV D, MELESHKO D, et al. Using SPAdes de novo assembler[J]. Curr Protoc Bioinform, 2020, 70(1): e102. DOI:10.1002/cpbi.102.
[33] JACKMAN S D, VANDERVALK B P, MOHAMADI H, et al. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter[J]. Genome Res, 2017, 27(5): 768-777. DOI:10.1101/gr.214346.116.
[34] ZERBINO D R, BIRNEY E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs[J]. Genome Res, 2008, 18(5): 821-829. DOI:10.1101/gr.074492.107.
[35] GRABHERR M G, HAAS B J, YASSOUR M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nat Biotechnol, 2011, 29(7): 644-652. DOI:10.1038/nbt.1883.
[36] CHIKHI R, RIZK G. Space-efficient and exact de Bruijn graph representation based on a bloom filter[J]. Lecture Notes in Computer Science(including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2012, 7534 LNBI: 236-248.
[37] FAIRCLOTH B C. Illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming[J]. 2013, http://dx.doi.org/10.6079/J9ILL.
[38] ZHANG F, DING Y, ZHU C D, et al.Phylogenomics from low-coverage whole-genome sequencing[J]. Mtthods Ecol Evol, 2019,10(4): 507-517. DOI: 10.1111/2041-210X.13145.
[39] FOROUZAN E, MALEKI M S M, KARKHANE A A, et al. Evaluation of nine popular de novo assemblers in microbial genome assembly[J]. J Microbiol Methods, 2017, 143: 32-37. DOI:10.1016/j.mimet.2017.09.008.
[40] SALZBERG S L, PHILLIPPY A M, ZIMIN A, et al. GAGE: a critical evaluation of genome assemblies and assembly algorithms[J]. Genome Res, 2012, 22(3): 557-567. DOI: 10.1101/gr.131383.111.
[41] ABBAS M M, MALLUHI Q M, BALAKRISHNAN P. Assessment of de novo assemblers for draft genomes: a case study with fungal genomes[J]. BMC Genomics, 2014, 15(Suppl.9): 10. DOI:10.1186/1471-2164-15-S9-S10. (