Phylogenetic inference using transcriptomic data

There have been several transcriptomics technologies used to gather sequence information on transcriptomes. However the most widely used is RNA-Seq.

RNA reads may be obtained using a variety of RNA-seq methods.

There are a number of public databases that contain freely available RNA-Seq data.

RNA-Seq data may be directly assembled into transcripts using sequence assembly.

Two main categories of sequence assembly are often distinguished:

1. de novo transcriptome assembly - especially important when a reference genome is not available for a given species.
2. Genome-guided assembly (sometimes mapping or reference-guided assembly) - is capable of using a pre-existing reference to guide the assembly of transcripts

Both methods attempt to generate biologically representative isoform-level constructs from RNA-seq data and generally attempt to associate isoforms with a gene-level construct. However, proper identification of gene-level constructs may be complicated by recent duplications, paralogs, alternative splicing or gene fusions. These complications may also cause downstream issues during ortholog inference. When selecting or generating sequence data, it is also vital to consider the tissue type, developmental stage and environmental conditions of the organisms. Since the transcriptome represents a snapshot of gene expression, minor changes to these conditions may significantly affect which transcripts are expressed. This may detrimentally affect downstream ortholog detection.

RNA may also be acquired from public databases, such as GenBank, RefSeq, [https://sites.google.com/a/ualberta.ca/onekp/ 1000 Plants (1KP)] and [http://www.1kite.org/ 1KITE]. Public databases potentially offer curated sequences which can improve inference quality and avoid the computational overhead associated with sequence assembly.

Orthology or paralogy inference requires an assessment of sequence homology, usually via sequence alignment. Phylogenetic analyses and sequence alignment are often considered jointly, as phylogenetic analyses using DNA or RNA require sequence alignment and alignments themselves often represent some hypothesis of homology. As proper ortholog identification is pivotal to phylogenetic analyses, there are a variety of methods available to infer orthologs and paralogs.{{cite journal|last1=Salichos|first1=Leonidas|last2=Rokas|first2=Antonis|last3=Fairhead|first3=Cecile|title=Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade|journal=PLOS ONE|date=13 April 2011|volume=6|issue=4|pages=e18755|doi=10.1371/journal.pone.0018755|pmid=21533202|pmc=3076445|doi-access=free|bibcode=2011PLoSO...618755S }}

These methods are generally distinguished as either graph-based algorithms or tree-based algorithms. Some examples of graph-based methods include InParanoid,{{cite journal|last1=Ostlund|first1=G.|last2=Schmitt|first2=T.|last3=Forslund|first3=K.|last4=Kostler|first4=T.|last5=Messina|first5=D. N.|last6=Roopra|first6=S.|last7=Frings|first7=O.|last8=Sonnhammer|first8=E. L. L.|title=InParanoid 7: new algorithms and tools for eukaryotic orthology analysis|journal=Nucleic Acids Research|date=5 November 2009|volume=38|issue=Database|pages=D196–D203|doi=10.1093/nar/gkp931|pmc=2808972|pmid=19892828}} MultiParanoid,{{cite journal|last1=Alexeyenko|first1=A.|last2=Tamas|first2=I.|last3=Liu|first3=G.|last4=Sonnhammer|first4=E. L.L.|title=Automatic clustering of orthologs and inparalogs shared by multiple proteomes|journal=Bioinformatics|date=27 July 2006|volume=22|issue=14|pages=e9–e15|doi=10.1093/bioinformatics/btl213|pmid=16873526|doi-access=free}} OrthoMCL,{{cite journal|last1=Li|first1=L.|title=OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes|journal=Genome Research|date=1 September 2003|volume=13|issue=9|pages=2178–2189|doi=10.1101/gr.1224503|pmc=403725|pmid=12952885}} HomoloGene{{cite journal|last1=Sayers|first1=E. W.|last2=Barrett|first2=T.|last3=Benson|first3=D. A.|last4=Bolton|first4=E.|last5=Bryant|first5=S. H.|last6=Canese|first6=K.|last7=Chetvernin|first7=V.|last8=Church|first8=D. M.|last9=DiCuccio|first9=M.|last10=Federhen|first10=S.|last11=Feolo|first11=M.|last12=Fingerman|first12=I. M.|last13=Geer|first13=L. Y.|last14=Helmberg|first14=W.|last15=Kapustin|first15=Y.|last16=Landsman|first16=D.|last17=Lipman|first17=D. J.|last18=Lu|first18=Z.|last19=Madden|first19=T. L.|last20=Madej|first20=T.|last21=Maglott|first21=D. R.|author-link21=Donna R. Maglott|last22=Marchler-Bauer|first22=A.|last23=Miller|first23=V.|last24=Mizrachi|first24=I.|last25=Ostell|first25=J.|last26=Panchenko|first26=A.|last27=Phan|first27=L.|last28=Pruitt|first28=K. D.|last29=Schuler|first29=G. D.|last30=Sequeira|first30=E.|last31=Sherry|first31=S. T.|last32=Shumway|first32=M.|last33=Sirotkin|first33=K.|last34=Slotta|first34=D.|last35=Souvorov|first35=A.|last36=Starchenko|first36=G.|last37=Tatusova|first37=T. A.|last38=Wagner|first38=L.|last39=Wang|first39=Y.|last40=Wilbur|first40=W. J.|last41=Yaschenko|first41=E.|last42=Ye|first42=J.|title=Database resources of the National Center for Biotechnology Information|journal=Nucleic Acids Research|date=21 November 2010|volume=39|issue=Database|pages=D38–D51|doi=10.1093/nar/gkq1172|pmid=21097890|pmc=3013733}} and OMA.{{cite journal|last1=Altenhoff|first1=A. M.|last2=kunca|first2=N.|last3=Glover|first3=N.|last4=Train|first4=C.-M.|last5=Sueki|first5=A.|last6=Pili ota|first6=I.|last7=Gori|first7=K.|last8=Tomiczek|first8=B.|last9=Muller|first9=S.|last10=Redestig|first10=H.|last11=Gonnet|first11=G. H.|last12=Dessimoz|first12=C.|title=The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements|journal=Nucleic Acids Research|date=15 November 2014|volume=43|issue=D1|pages=D240–D249|doi=10.1093/nar/gku1158|pmid=25399418|pmc=4383958|doi-access=free}} Tree-based algorithms include programs such as OrthologID or RIO.{{cite journal|last1=Zmasek|first1=Christian M|last2=Eddy|first2=Sean R|title=RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs|journal=BMC Bioinformatics|date=2002|volume=3|issue=1|pages=14|doi=10.1186/1471-2105-3-14|pmid=12028595|pmc=116988|doi-access=free}}

A variety of BLAST methods are often used to detect orthologs between species as a part of graph-based algorithms, such as MegaBLAST, BLASTALL, or other forms of all-versus-all BLAST and may be nucleotide- or protein-based alignments.{{cite journal|last1=Barker|first1=M. S.|last2=Vogel|first2=H.|last3=Schranz|first3=M. E.|title=Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales|journal=Genome Biology and Evolution|date=5 October 2009|volume=1|pages=391–399|doi=10.1093/gbe/evp040|pmid=20333207|pmc=2817432|doi-access=free}}{{cite journal|last1=Yang|first1=Xu|last2=Cheng|first2=Yu-Fu|last3=Deng|first3=Cao|last4=Ma|first4=Yan|last5=Wang|first5=Zhi-Wen|last6=Chen|first6=Xue-Hao|last7=Xue|first7=Lin-Bao|title=Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis|journal=BMC Genomics|date=2014|volume=15|issue=1|pages=412|doi=10.1186/1471-2164-15-412|pmid=24885385|pmc=4070557|doi-access=free}} RevTrans{{cite journal|last1=Wernersson|first1=R.|title=RevTrans: multiple alignment of coding DNA from aligned amino acid sequences|journal=Nucleic Acids Research|date=1 July 2003|volume=31|issue=13|pages=3537–3539|doi=10.1093/nar/gkg609|pmid=12824361|pmc=169015|doi-access=free}} will even use protein data to inform DNA alignments, which can be beneficial for resolving more distant phylogenetic relationships. These approaches often assume that best-reciprocal-hits passing some threshold metric(s), such as identity, E-value, or percent alignment, represent orthologs and may be confounded by incomplete lineage sorting.{{cite journal|last1=Moreno-Hagelsieb|first1=G.|last2=Latimer|first2=K.|title=Choosing BLAST options for better detection of orthologs as reciprocal best hits|journal=Bioinformatics|date=26 November 2007|volume=24|issue=3|pages=319–324|doi=10.1093/bioinformatics/btm585|pmid=18042555|doi-access=free}}{{cite journal|last1=Castillo-Ramírez|first1=Santiago|last2=González|first2=Víctor|title=Factors affecting the concordance between orthologous gene trees and species tree in bacteria|journal=BMC Evolutionary Biology|date=2008|volume=8|issue=1|pages=300|doi=10.1186/1471-2148-8-300|pmid=18973688|pmc=2614993|doi-access=free|bibcode=2008BMCEE...8..300C }}

It is important to note that orthology relationships in public databases typically represent gene-level orthology and do not provide information concerning conserved alternative splice variants.

Databases that contain and/or detect orthologous relationships include:

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• [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DIOPT]
• [http://www.ensembl.org/info/genome/compara/ Ensembl Compara]
• [http://www.greenphyl.org/ GreenPhylDB]
• [http://www.deep-phylogeny.org/hamstr/ HaMStR]
• [https://www.ncbi.nlm.nih.gov/homologene HomoloGene]
• [http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid]
• [http://multiparanoid.sbc.su.se/ MultiParanoid]
• [http://omabrowser.org/ OMA]
• OrthoDB
• OrthoFinder
• [https://web.archive.org/web/20140224164715/http://nypg.bio.nyu.edu/orthologid/ OrthologID]
• [http://orthomcl.org/orthomcl/ OrthoMCL]
• [http://www.pathogenomics.sfu.ca/ortholugedb OrtholugeDB]
• [http://phylomedb.org/ PhylomeDB]
• [http://www.treefam.org/ TreeFam]
• [http://eggnogdb.embl.de eggNOG]
• [http://metaphors.phylomedb.org/ metaPhOrs]

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As eukaryotic transcription is a complex process by which multiple transcripts may be generated from a single gene through alternative splicing with variable expression, the utilization of RNA is more complicated than DNA. However, transcriptomes are cheaper to sequence than complete genomes and may be obtained without the use of a pre-existing reference genome.{{cite book|last1=Hörandl|first1=Elvira|last2=Appelhans|first2=Mark|title=Next-generation sequencing in plant systematics|date=2015|publisher=Koeltz Scientific Books|isbn=9783874294928}}

It is not uncommon to translate RNA sequence into protein sequence when using transcriptomic data, especially when analyzing highly diverged taxa. This is an intuitive step as many (but not all) transcripts are expected to code for protein isoforms. Potential benefits include the reduction of mutational biases and a reduced number of characters, which may speed analyses. However, this reduction in characters may also result in the loss of potentially informative characters.

There are a number of tools available for multiple sequence alignment. All of which possess their own strengths and weaknesses and may be specialized for distinct sequence types (DNA, RNA or protein). As such, a splice-aware aligner may be ideal for aligning RNA sequences, whereas an aligner that considers protein structure or residue substitution rates may be preferable for translated RNA sequence data.

Using RNA for phylogenetic analysis comes with its own unique set of strengths and weaknesses.

• large set of characters
• cost-effective
• not dependent upon a reference genome

• expenses of extensive taxon sampling
• difficulty in identification of full-length, single-copy transcripts and orthologs
• potential misassembly of transcripts (especially when duplicates are present)
• missing data as a product of the transcriptome representing a snapshot of expression or incomplete lineage sorting{{cite journal|last1=Wen|first1=Jun|last2=Xiong|first2=Zhiqiang|last3=Nie|first3=Ze-Long|last4=Mao|first4=Likai|last5=Zhu|first5=Yabing|last6=Kan|first6=Xian-Zhao|last7=Ickert-Bond|first7=Stefanie M.|last8=Gerrath|first8=Jean|last9=Zimmer|first9=Elizabeth A.|last10=Fang|first10=Xiao-Dong|last11=Candela|first11=Hector|title=Transcriptome Sequences Resolve Deep Relationships of the Grape Family|journal=PLOS ONE|date=17 September 2013|volume=8|issue=9|pages=e74394|doi=10.1371/journal.pone.0074394|pmid=24069307|pmc=3775763|doi-access=free|bibcode=2013PLoSO...874394W }}

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• BLAST
• Coding region
• Computational phylogenetics
• De novo transcriptome assembly
• Exome
• Exome sequencing
• Expressed sequence tag
• Gene expression
• Homology
• List of phylogenetics software
• Phylogenetics
• Phylogenetic tree
• RNA
• RNA-Seq
• Sequence alignment
• Synonymous substitution
• Systematics
• Transcriptome
• UniGene

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{{reflist|2}}

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• [http://www.1kite.org/ 1KITE]
• [https://sites.google.com/a/ualberta.ca/onekp/ 1000 Plants (1KP)]
• [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DIOPT]
• [http://eggnogdb.embl.de eggNOG]
• [http://www.ensembl.org/info/genome/compara/ Ensembl Compara]
• [https://www.ncbi.nlm.nih.gov/genbank/ GenBank]
• [http://www.greenphyl.org/ GreenPhylDB]
• [http://www.deep-phylogeny.org/hamstr/ HaMStR]
• [https://www.ncbi.nlm.nih.gov/homologene HomoloGene]
• [http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid]
• [http://multiparanoid.sbc.su.se/ MultiParanoid]
• [http://metaphors.phylomedb.org/ metaPhOrs]
• [https://www.ncbi.nlm.nih.gov/BLAST/ NCBI_BLAST]
• [http://omabrowser.org/ OMA]
• [http://www.orthodb.org/ OrthoDB]
• [https://web.archive.org/web/20140224164715/http://nypg.bio.nyu.edu/orthologid/ OrthologID]
• [http://orthomcl.org/orthomcl/ OrthoMCL]
• [http://www.pathogenomics.sfu.ca/ortholugedb OrtholugeDB]
• [http://phylomedb.org/ PhylomeDB]
• [https://www.ncbi.nlm.nih.gov/refseq/ RefSeq]
• [http://www.cbs.dtu.dk/services/RevTrans-2.0/web/ RevTrans_2.0]
• [http://www.treefam.org/ TreeFam]
• [https://github.com/trinityrnaseq/trinityrnaseq/wiki Trinity_de_novo_assembler]

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Category:Computational phylogenetics

Category:Genetics techniques