De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis
© Zeng et al; licensee BioMed Central Ltd. 2011
Received: 10 August 2011
Accepted: 25 November 2011
Published: 25 November 2011
Arthropods are the most diverse animal phylum, but their genomic resources are relatively few. While the genome of the branchiopod Daphnia pulex is now available, no other large-scale crustacean genomic resources are available for comparison. In particular, genomic resources are lacking for the most tractable laboratory model of crustacean development, the amphipod Parhyale hawaiensis. Insight into shared and divergent characters of crustacean genomes will facilitate interpretation of future developmental, biomedical, and ecological research using crustacean models.
To generate a transcriptome enriched for maternally provided and zygotically transcribed developmental genes, we created cDNA from ovaries and embryos of P. hawaiensis. Using 454 pyrosequencing, we sequenced over 1.1 billion bases of this cDNA, and assembled them de novo to create, to our knowledge, the second largest crustacean genomic resource to date. We found an unusually high proportion of C2H2 zinc finger-containing transcripts, as has also been reported for the genome of the pea aphid Acyrthosiphon pisum. Consistent with previous reports, we detected trans-spliced transcripts, but found that they did not noticeably impact transcriptome assembly. Our assembly products yielded 19,067 unique BLAST hits against nr (E-value cutoff e-10). These included over 400 predicted transcripts with significant similarity to D. pulex sequences but not to sequences of any other animal. Annotation of several hundred genes revealed P. hawaiensis homologues of genes involved in development, gametogenesis, and a majority of the members of six major conserved metazoan signaling pathways.
The amphipod P. hawaiensis has higher transcript complexity than known insect transcriptomes, and trans-splicing does not appear to be a major contributor to this complexity. We discuss the importance of a reliable comparative genomic framework within which to consider findings from new crustacean models such as D. pulex and P. hawaiensis, as well as the need for development of further substantial crustacean genomic resources.
Crustaceans are one of the four major groups that make up the phylum Arthropoda, the most speciose and morphologically diverse animal group . Despite the fact that arthropods as a whole make up the majority of animal species diversity and biomass, until recently the only arthropod represented in the list of NIH model organisms http://www.nih.gov/science/models/ was the fruit fly Drosophila melanogaster. The water flea Daphnia pulex was recently added to this list, and is the only crustacean to date with a publicly accessible sequenced genome . As crustaceans are now widely recognized as sister group to the hexapods [3–7], the phylogenetic position of D. pulex suggests that it could serve as a useful outgroup to insects, providing meaningful comparisons with the many insights into developmental and disease biology provided by work on D. melanogaster. However, there are no genomic resources on a scale comparable to the D. pulex genome, and so it is still not known to what extent the characteristics of the water flea genome are specific to this animal's ecology or shared by other crustaceans . Moreover, comparisons of biomedically relevant processes and mechanisms between D. pulex and other model organisms must be informed by robust phylogenetic hypotheses. At the moment, which specific subgroup of crustaceans is closest to the hexapods (including D. melanogaster) is still a matter of debate , but several phylogenetic hypotheses suggest that branchiopods may be more distant from insects than other crustacean groups [6, 9–12].
Crustaceans have long been the subject of ecological and evolutionary study, as well as being lucrative commercial species for human consumption. Even for many of the most intensively studied of these , surprisingly few genomic projects have been reported. Most of the crustacean EST projects completed to date, notably for the farmed shrimp Litopenaeus vannamei (~163,000 ESTs) [14–16], the salmon ectoparasite copepod Lepeophtheirus salmonis (~129,000 ESTs) , the porcelain crab Petrolisthes cinctipes (~98,000 ESTs) , and the lobster Homarus americanus (~52,000 ESTs) [19–21], have all used Sanger sequencing of cDNA libraries. Next generation sequencing technologies are increasingly affordable, accessible and robust even for organisms lacking a sequenced genome , but have been reported to be applied to a crustacean de novo transcriptome only once, in the Antarctic krill Euphausia superba. This organism is the subject of ecological and climate change research, but is not a viable laboratory model organism due to its specialized habitat.
While new understanding of developmental and molecular mechanisms in D. pulex are expected to follow from its genome sequence, it is important to note that crustaceans have been the subject of comparative embryology for over a century , and in recent decades, of evolutionary developmental biology ("evo-devo"). The morphological and molecular mechanistic variations of early embryogenesis, modifications of their body plans and appendage diversifications displayed by crustaceans have all been the subject of studies too numerous to describe here. However, until recently most comparative analyses of crustaceans have been limited to the study of gene expression or experimental embryology, as crustacean models where functional genetic testing is possible are still few in number. The limiting factor for comparative functional experiments is often obtaining specific coding sequences of sufficient length. A large-scale genomic resource for a model crustacean would therefore greatly facilitate development and deployment of transgenic tools.
The amphipod Parhyale hawaiensis has emerged as an important laboratory model crustacean species over the last several years . P. hawaiensis was first described in the Hawaiian islands , but it occupies intertidal marine habitats worldwide. Laboratory husbandry is easy and affordable, and inbred lab cultures produce hundreds of embryos year-round, providing ample material for developmental studies. Fate map and cell lineage analyses of the early embryo show that all three germ layers and the germ line are determined by the eight cell stage , and clonal populations show predictable patterns at least up until gastrulation . Despite this apparently "mosaic" embryonic development, significant regulative properties have also been described for the embryonic mesoderm and ectoderm . Molecular techniques for the study of development, including stable transgenesis [29–31] and gene knockdown [32–34] are arguably better established for P. hawaiensis than for any other laboratory crustacean model.
However, the number of P. hawaiensis developmental genes available as GenBank accessions is less than 25. Progress in understanding the development of P. hawaien sis is thus is limited by the relative paucity of publicly available cloned coding and regulatory regions. Indeed, since the development of germ line transgenesis in P. hawaiensis, its use in developmental studies has been reported only three times [30, 31, 34].
Analysis of phenotypes of genomic transgene insertions  and case studies of intron sizes  are consistent with an extremely large genome size for this amphipod. Accordingly, the genome size of P. hawaiensis is estimated to be 2.98 Gb (, R. Gregory and C. Extavour, unpublished), very near that of Homo sapiens[36, 37]. A genomic BAC library for P. hawaiensis has been created and partially sequenced  but is not yet available in GenBank. The genome of the closely related amphipod Jassa marmorata, with a much smaller genome of 690 Mbp (~4 times the size of the D. melanogaster genome) has been approved for whole genome, BAC end, and EST sequencing by the Joint Genome Institute , but this work is still ongoing, and laboratory culture of this amphipod is difficult. A large transcriptome dataset for P. hawaiensis would thus be a highly valuable resource for several scientific communities, and would in addition assist with the annotation of planned amphipod genomic projects. Recent construction of a de novo transcriptome for the milkweed bug Oncopeltus fasciatus, which also lacks a sequenced genome , suggested that 454 pyrosequencing would be a fruitful approach to obtaining a large scale P. hawaiensis transcriptome.
Here we present the de novo assembly of a maternal and embryonic transcriptome for P. hawaiensis, sequenced with 454 Titanium pyrosequencing. We describe particular features of the P. hawaiensis transcriptome that were revealed during assembly and annotation, including the presence of trans-splicing and enrichment for C2H2 Zn finger domain-containing transcripts. We annotate orthologues of genes involved in several major developmental patterning processes, gametogenesis in males and females, and members of major conserved animal signaling pathways. We observe a high proportion of apparently unique sequences in the transcriptome, and discuss these findings in the light of observations on the D. pulex genome and other existing crustacean genomic resources.
Results and Discussion
Collection and preparation of material for ovarian and embryonic cDNA libraries
Sequencing and assembly of the P. hawaiensis transcriptome
P. hawaiensis transcriptome assembly statistics
Raw reads (base pairs)
Singletons (% of assembled reads)
# Unique BLAST hits
Mean # isotigs per isogroup
Newbler Contigs ("exons")
Mean # contigs per isotig
The default parameters of Newbler v2.5 were used to screen for adapters and eliminate poor quality reads. The resulting 3,157,373 reads (99.5% of raw reads) were then assembled (Table 1). 2,349,266 (74.4%) of the screened reads were incorporated into assembled sequences (isotigs or contigs), with 276,564 (8.8%) singletons remaining. 531,543 reads (16.8% of reads subjected to assembly) were excluded because they were only partially assembled (431,372; 13.7%), from repeat regions (5,022; 0.2%), outliers (86,822; 2.7%), or too short (< 40 bp: 8,327; 0.3%). The assembly contained 89,664 contigs, which grouped into 35,301 isotigs. 18,615 (52.7%) of these isotigs were made up of only one contig, and the average number of contigs per isotigs was 2.1. The isotig N50 length was 1,510 bp, and the number of isogroups was 25,735 (18,565 (72.1%) of these comprised only one isotig, and the mean number of isotigs per isogroup was 1.4). The average coverage per contig was 7.1 reads/bp (Additional File 3). Averaging across all bases in the entire assembly, the average coverage per base pair was 25.4, meaning that every base pair in the transcriptome was sequenced 25.4 times on average. This coverage is high compared to typical numbers for de novo transcriptome assemblies, and should be helpful for distinguishing SNPs and indels from potential sequencing errors in raw reads . Fasta files of all assembly products are freely available from the authors.
BLAST mapping of non-redundant transcriptome sequences
P. hawaiensis transcriptome BLAST results
# BLAST hits against nr1(%)
# Unique BLAST hits against nr1(%)
Total Non-Redundant Assembly Sequences (= isotigs + singletons)
Transcriptome Gene Ontology (GO) term annotation
Unusual characteristics of the P. hawaiensis transcriptome
P. hawaiensis has been found to employ trans-splicing among its genetic regulatory mechanisms . In this mechanism, sections of transcripts transcribed from independent genomic loci are spliced together post-transcriptionally to form a novel transcript. Such trans-spliced transcripts are recognizable because they contain a diagnostic splice-leader sequence. We wished to determine to what extent this additional transcript complexity affected our assembly and our ability to assign high-confidence BLAST annotations. We therefore processed the trimmed, pre-assembly reads to remove those containing the diagnostic splice-leader sequences (2,584; 0.1%), and performed a Newbler v2.5 assembly on the remaining reads. The results of this assembly were not noticeably different from the complete assembly, nor did the number of unique BLAST hits increase (Additional File 4). We therefore concluded that the presence of trans-spliced transcripts did not significantly affect our transcriptome assembly or annotation.
When we considered the species identity of the top BLAST hit for each isotig and singleton (see Methods), we found that a high proportion (50.5%) of our assembly sequences most closely matched sequences from other arthropods (Additional File 5). However, an unexpectedly high proportion (12.2%) was from the lancelet Branchiostoma floridae, which is phylogenetically very far removed from P. hawaiensis. When we examined those sequences with a lancelet sequence as top hit, we noticed that (a) for many of them, the top 50 BLAST hits were all B. floridae; and (b) the majority of them seemed to contain C2H2 zinc fingers with a specific linker sequence (TGEKP) between C2H2 domains.
Comparison with other arthropod genomic resources
The BLAST hit rate of the P. hawaiensis isotigs was 29.5%. This is higher than those reported in other de novo transcriptome analyses [40–45], including that of an arctic crustacean , but much lower than the 43.4% obtained from a previously analyzed de novo insect maternal/embryonic transcriptome . The ~70% of P. hawaiensis isotigs without a high confidence BLAST hit could be either P. hawaiensis-specific genes, or genes with relatively lower similarity to known genes. In addition, it is possible that many of our transcripts represent untranslated sequences rather than coding regions (for example, UTRs or noncoding RNAs), and therefore do not match nr protein sequences.
The relatively low proportion of hits may also reflect the fact that until recently (and including the version of nr we used for our analysis, which did not include the D. pulex genome at the time of analysis) very few crustacean sequences were included in nr. The D. pulex genome also contains a high proportion (~36%) of apparently Daphnia-specific genes, thought to be largely the result of amplification of selected gene families . Noting that the E-value cutoff used for the D. pulex analyses (1e-5) was slightly more relaxed than that used in our initial analysis (1e-10), we repeated the BLASTX of our non-redundant P. hawaiensis transcriptome sequences against nr with an E-value cutoff of 1e-5. This yielded 26,494 unique BLAST hits (including 34.8% of isotigs and 5.7% of singletons). We therefore found that even adjusting the E-value cutoff to that used for characterization of the D. pulex genome, ~59% of the sequences in this P. hawaiensis transcriptome lack significant similarity to other characterized animal sequences. These observations suggest that crustaceans may have more species- or clade-specific genes than previously appreciated. Alternatively, these high numbers of apparently lineage-restricted genes may simply reflect the paucity of crustacean genomic resources currently in public databases.
Those P. hawaiensis transcriptome sequences which failed to obtain a significant BLAST hit when compared with nr might share more similarity with other crustaceans. To test this, we used BLAST to compare all P. hawaiensis transcriptome sequences that had failed our 1e-10 E-value cutoff against nr, with the predicted D. pulex transcriptome (see Methods) using BLASTX and a 1e-10 E-value cutoff. We then used BLAST to compare the obtained sequences with nr to determine their putative identities. We did not set an E-value limit for this second BLAST, in order to recover at least some minimal information about the identity of these genes (E-values for a subset of these, described below, are shown in Additional File 6). We found that 47.9% of these sequences came from arthropods, only 2.5% of which were crustaceans. The low crustacean representation in nr makes it difficult to obtain high confidence BLAST hits for this group. We therefore focused on determining what proportion of "nr orphan" P. hawaiensis sequences were highly similar to sequences from D. pulex by comparing the E-values for BLAST hits against both nr and against the D. pulex predicted transcriptome. We found that of the 423 P. hawaiensis sequences with higher similarity to D. pulex genes than to anything in nr (Additional File 6), 381 (90.1%) of these had E-values at least an order of magnitude higher for D. pulex compared to nr, and 30 of these (7.1% of total) had E-values greater than one for nr hits, but D. pulex hit E-values of 1e-11 or lower. Most of this "Daphnia-like" group matched arthropod sequences that were previously annotated as "hypothetical proteins," suggesting that non-insect crustacean sequence annotation could improve future annotation of the existing insect genomes.
The D. pulex genome has been found to contain a high number of genes (at least 30,907) . Without a genome sequence for P. hawaiensis, we cannot accurately estimate gene number in order to perform a rigorous comparison with D. pulex. However, our transcriptome assembly identified 25,735 isogroups. Because isogroups are groups of isotigs assembled from the same set of contigs, isogroups may represent putative genes, with each isotig of the isogroup representing a transcript variant, for example a splice variant. We therefore speculate that P. hawaiensis, with a genome over one order of magnitude larger than that of D. pulex (C. Extavour & R. Gregory, unpublished), may also have a high gene number of at least 25,735 genes.
However, using isogroup number of this de novo transcriptome as a proxy for total gene number has two significant limitations. The first is the result of our chosen tissue sampling strategy: this transcriptome does not capture postembryonic gene expression. After hatching, expression of several genes with exclusively juvenile or adult roles is likely, including at minimum additional genes associated with molting, behavior, and gametogenesis. It is therefore possible that the number of isogroups in our assembly underestimates the true gene number in P. hawaiensis.
The second limitation is the unavoidable result of any de novo assembly, which is that if two sequences from the same transcript do not share significant overlap, they will appear as separate assembly products rather than as a single transcript (see also discussion of unique BLAST hit number in section "BLAST mapping of non-redundant transcriptome sequences" above). This could result in the number of isogroups being an overestimate of the true number of genes. A further complication results from Newbler v2.5's method of handling isogroups made of multiple isotigs. When we performed our assembly, we limited the number of isotigs in one isogroup to 10 ("-it" flag; see Methods). This has the advantage of avoiding isogroups composed of large numbers of isotigs, as we suspect that in P. hawaiensis, as shown for other animals, the vast majority of genes have fewer than ten splicing isoforms . However, it can also result in problematic isogroup number calculation, because isogroups that exceed the number of isotigs per isogroup threshold are returned to the assembly file as contigs rather than isotigs, thus inflating the gene number estimate. In summary, in order to determine whether high numbers of species- or clade-specific genes is a general characteristic of crustaceans, and the true extent of species-specific genes for P. hawaiensis, more deep genomic resources will have to be developed for this amphipod and for more crustaceans of diverse classes.
Assessment of depth and transcript coverage of the transcriptome
Total isotig length increased steadily as progressively larger subsets of reads were assembled (Figure 6B). While small numbers of isotigs over 4,500 bp could be obtained with as few as ~300,000 reads, robust recovery of isotigs longer than 6,500 bp required assembly of at least 60% of our total reads, or ~1.9 million reads. This demonstrates that increased depth of sequencing, in addition to improving gene discovery, has the added benefit of increasing predicted transcript lengths, thereby facilitating their annotation and making them more immediately useful for downstream applications. In a related analysis, we searched the transcriptome for the presence of the small number of P. hawaiensis developmental genes available as GenBank accessions, and found that 52.4% (11/21) were present (Additional File 7). However, only for one of these genes (Ph-prospero) did our transcriptome add sequence data to the GenBank accession (Additional File 8). This may be a reflection of both the relatively rarity of these transcripts, and the fact that those genes identified to date have been the subject of intense developmental studies, and so sequences of considerable length have already been cloned to close to full length [30, 34, 52–57].
Annotation of signaling pathway genes
Annotation of developmental and gametogenesis genes
Given the tractability of P. hawaiensis as a developmental model, we sought to make this transcriptome of maximal immediate use to the amphipod and broader developmental biology and biomedical research communities. We therefore undertook manual annotation of over 450 genes involved in embryonic patterning, developmental pathways (Additional File 10) and gametogenesis in both males and females (Additional File 11). We used lists of genes known to function in these processes in Drosophila as a starting point http://www.sdbonline.org/fly/aimain/1aahome.htm, and identified over 200 likely P. hawaiensis homologues of these genes. As we observed for our annotation of signaling pathway genes, the majority of matching transcriptome reads are of sufficient length to allow immediate use in gene expression and function studies.
Several of the genes contained multiple hits in our transcriptome, including a large number of singletons. For some genes, these multiple hits included consecutively numbered isotigs with very similar lengths. We examined a subset of these genes to determine whether or not these apparently highly similar isotigs were in fact different from each other. We found that such sequences usually differed from each other at a small number of nucleotide positions, either because of low sequencing quality in one of the component reads, or because of SNPs or small indels (Additional File 12). Although annotation of SNPs in this transcriptome is beyond the scope of this study, we anticipate that the SNPs present in this transcriptome could serve as a useful tool for population-level variation studies in the future.
We have generated a maternal and embryonic transcriptome of the amphipod crustacean Parhyale hawaiensis using 454 Titanium pyrosequencing. To our knowledge, this represents the second largest crustacean genomic resource, behind the genome of the cladoceran D. pulex, and the largest de novo assembled pyrosequencing-based transcriptome to date. We confirmed the previously reported presence of trans-splicing in P. hawaiensis, but found that the presence of these trans-spliced transcripts did not greatly increase the complexity of the transcriptome or impede assembly. The P. hawaiensis transcriptome appears to be enriched for a particular class of C2H2 Zn finger-coding transcripts, which share high similarity with several Branchiostoma floridae transcripts, and is also reported to be an enriched sequence class in the genome of the pea aphid Acyrthosiphon pisum.
We annotated the de novo transcriptome for a large number of developmentally relevant genes, including major conserved metazoan signaling pathways. We found that even after assembly of over 3 million reads, gene discovery continued to increase, suggesting that the extremely large genome size of this amphipod may reflect high gene numbers, high transcript complexity, or both. These data should both facilitate future developmental and evolutionary studies using this emerging model crustacean species, and contribute to future work in crustacean comparative genomics.
The bulk of existing arthropod genomic resources are for insects, while the sister group to the insects, the crustaceans, remains relatively unexplored. The large genome size and low relative similarity to existing annotated arthropod genomes may be challenges to potential future efforts to sequence the P. hawaiensis genome. However, high throughput short read sequencing technologies such as Illumina or SOLiD , combined with the transcriptome described here, should make such projects tractable.
Finally, this dataset should assist phylogenomic approaches to resolution of controversies in crustacean phylogenetic relationships, including the relationship between crustaceans and hexapods. D. pulex belongs to the Branchiopoda, and while some phylogenetic analyses place this group closest to the hexapods [62–65], others suggest that the Malacostraca (the group including P. hawaiensis and most edible crustaceans such as shrimp, lobster and crab) are sister to the hexapods [4, 9–11, 66]. Yet others suggest that Branchiopoda may be the most derived group within a monophyletic clade containing all crustaceans except for Malacostraca, Remipedia and Cephalocarida . The largest phylogenomic assessment of this problem to date places both Branchiopoda and Malacostraca in a monophyletic clade that is sister to a (Hexapoda + Remipedia + Cephalocarida) clade . Moreover, Daphnia species do not branch basally within the Branchiopoda, and indeed are placed in the most derived branchiopod clade by most phylogenetic analyses [6, 68, 69]. These competing hypotheses emphasize the importance of a reliable comparative genomic framework within which to consider findings from new crustacean models. In order to place future comparative, ecological, environmental and biomedical studies using crustacean models in an appropriate phylogenetic context, additional crustacean genomic resources will be necessary.
The P. hawaiensis (Figure 1A, B) specimens sequenced in this study were from an inbred, non-backcrossed, non-isogenic laboratory culture originally obtained from Ernst Wimmer in 2002; the Wimmer culture in turn was obtained from a laboratory culture from Nipam H. Patel that was established with animals from the John G. Shedd Aquarium (Chicago, IL) as previously described . The animals were maintained in the laboratory in artificial seawater (Instant Ocean, specific gravity 1.018-1.022), and fed a mixture of raw carrots, TetraAlgae Vegetable Enhanced Crisps, TetraMin Tropical Flakes, and Hikari Wheat Germ Pellets. All cultures were maintained under a 12:12 light/dark cycle at 28°C.
471 mixed-stage embryos (Additional File 1; total weight 52.7 mg) representing the entirety of embryogenesis (Figure 1D) were shock frozen in liquid nitrogen and stored at -80°C. 30 ovaries (comprising eight small ovaries from young females and 22 late ovaries containing mature oocytes from older females; Figure 1C) were dissected from females in Trizol, flash frozen in Trizol, and stored at -80°C. Total RNA was isolated separately from ovaries (Figure 1C) and from mixed stages of embryogenesis (Figure 1E), and a pool was created of 1.5 μg of total RNA from each sample for use as a template for first strand cDNA synthesis (3 μg total). cDNA was synthesized following a protocol developed specifically for 454 Titanium sequencing of cDNA , with the exception that none of the cDNA was normalized in the present study. This protocol is based on the SMART cDNA library construction kit (Clontech, CA, USA), and includes a modified poly(T) primer to enrich for mRNA, and a DNAse treatment step to remove possible genomic DNA contamination. Following first strand cDNA synthesis, primary amplification of the cDNA required thirteen PCR cycles to maximize yield while avoiding overcycling (monitored in real-time via qPCR ). Secondary amplification began to plateau after nine cycles. To obtain sufficient double-stranded cDNA for pyrosequencing sequencing (~5 μg) without overcycling, 26 reactions of 100 μg each were run in parallel and subsequently co-purified into 90 μl of elution buffer using QIAquick PCR purification columns (Qiagen Inc).
454 Titanium Pyrosequencing
The samples were nebulized, adaptor-ligated, and pyrosequenced using the GS-FLX Titanium platform by the Institute for Genome Science and Policy DNA Sequencing Facility (Duke University). All of the raw reads generated in this study have been submitted to the NCBI Short Read Archive (Study Accession Number: SRA021010).
Raw reads were assembled using the cDNA assembly algorithm (the "-cdna" flag) of Newbler v2.5. An adaptor-trimming step was included in the assembly (the "-vt" flag). Screening adaptors used are available at http://extavourlab.com/protocols/ExtavourLab_454_Adapters.fasta). A vector-screening step (the "-vs" flag) was performed using a FASTA version of the Univec database ftp://ftp.ncbi.nih.gov/pub/UniVec/. Due to the long average length of the raw 454 reads, the minimum overlapping length (the "-ml" flag) was set to the default value of 40 base pairs. To accommodate the possible existence of SNPs and pyrosequencing errors, the minimum identity between sequences (the "-mi" flag) was set to require 95% identity between aligned sequences. Trimmed singleton reads were specifically produced by Newbler (the "-trim" flag). A maximum isogroup size of 10 isotigs was specified (the "-it" flag) to prevent Newbler from constructing an isogroup using an overly large quantity of short contigs. The resulting assembled reads and unassembled singletons were used for all subsequent analyses.
Sequences were first mapped against the nr (all non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF) peptide sequence database [70, downloaded from ftp://ftp.ncbi.nih.gov/blast/db/on April 27, 2010] using BLASTX. Unless otherwise specified, all BLAST searches were conducted using BLAST v2.2.24+  with an E-value cutoff of 1e-10.
Due to the sequence depth of this project, the transcripts were assembled with the raw 454 reads were not all full-length. If sequences represent different regions of the same transcript that are not assembled together due to insufficient overlap, they run the risk of being counted twice in our BLAST annotation. To address this problem, a custom Perl script was created in order to estimate the number of unique transcripts present in the P. hawaiensis transcriptome (called "UniqueBlast.pl" available at http://www.extavourlab.com/protocols/bio_tools/Perl_Transcriptome_Analysis_Scripts.zip). UniqueBlast.pl utilizes the results of BLASTX against nr for all assembly products with an E-value cutoff of 1e-10, to predict whether multiple assembly products are fragments of the same transcript. UniqueBlast.pl accomplishes this by comparing the HSP region of assembly products with the same top BLAST hit. Assembly products that have the same top BLAST hit but non-overlapping HSP regions are considered as fragments of the same transcript. Assembly products with the same top BLAST hits and overlapping HSP regions are considered as putative isoforms or paralogues of each other. Overlapping is defined as greater than 14 amino acids shared within the HSP, because the assembly parameters require a minimum of 40 matching nucleotides in order for two raw reads to be assembled together. UniqueBlast.pl then generates a list of assembly sequences (isotigs or contigs) showing the longest fragment of each transcript, as well as predicted isoforms and paralogues. This list of unique transcripts was then used for all subsequent analysis including GO analysis, ortholog hit ratio calculations, and phylogenetic distribution analysis of top BLAST hit organisms.
For analysis of the phylogenetic distribution of species of top unique matches to non-redundant assembly sequences, we used BLASTX to compare our non-redundant assembly products (isotigs + singletons, see Table 2) with nr using an E-value cutoff of 1e-10. We discarded redundant hits as described using "UniqueBlast.pl." For each gene in this list of unique BLAST hits, we recorded the species identity of the top BLAST hit sequence. We then tallied the total numbers for clades of interest, shown in Figure 4 and Additional File 5. When assessing the effect of Branchiostoma floridae C2H2 Zn finger sequences on the annotation of the assemblies, we assessed top BLAST hits obtained with both the NCBI reference Sequence collection (RefSeq) and nr, and obtained comparable results for both searches.
For comparison of sequences belonging to different GO terms between species, we used the Oncopeltus fasciatus data from a previously generated transcriptome  and a precomputed GO annotation of the D. melanogaster genome . To obtain GO category data for Daphnia pulex, we used the transcripts predicted from the D. pulex genome (downloaded on 3 December 2010 from ftp://iubio.bio.indiana.edu/daphnia/genome/Daphnia_pulex/dpulex_jgi060905/fasta/dpulex-gnomon-transcript-jgi060905.fasta.gz).
To search for developmental genes of interest, we used TBLASTN with protein queries being the full length Drosophila melanogaster homologue of the gene of interest. For genes that yielded no hits when the D. melanogaster homologue was used as a query, homologues from other animals were used as queries. In cases where proteins possessed domains that were also shared by other genes from a different gene family (e.g. abstrakt: zinc finger domain), the TBLASTN search was performed by masking the relevant domain in the query sequence. Finally, in cases of genes with small, diagnostic conserved domains within an otherwise poorly conserved sequence, the diagnostic domains were used as the query (e.g. groucho). An E-value cutoff of e-10 was used for all BLAST searches, except for those searches with masked domains or specific protein domains, in which case the E-value cutoff was e-5. For all developmental genes found, species identity and domain details of the query used are indicated in the legends to Additional Files 9, 10 and 11.
Removal of reads from trans-spliced sequences
To determine how the presence of trans-spliced sequences affected our assembly with Newbler, we used the P. hawaiensis splice leader sequences [as per Figure 1 of 47] as an "adapter" sequence (the "-vs" flag) in the trimming step performed by Newbler prior to assembly. This resulted in removal or trimming of all raw reads containing the splice leader sequence. The remaining reads were assembled with Newbler v2.5 and compared using BLAST against nr as described for the complete assembly.
Removal of C2H2 Zinc finger-containing sequences
Because we suspected that specific characteristics of P. hawaiensis C2H2 Zn-finger containing proteins might be responsible for a high incidence of BLAST hits to sequences of the lancelet Branchiostoma floridae, we performed a new assembly after removing a subset of reads in the following way: we scanned all reads for the presence of C2H2 Zn finger-encoding sequences using the least stringent C2H2 motif defined in , which is X2-C-X1,2,4,5-C-X12-H-X3-6-(H,C). We used this least stringent criterion rather than the most stringent criterion defined by Böhm and colleagues, in order to capture the largest number of reads containing these motifs. We reasoned that even "C2H2-like" domains might result in a Zn finger BLAST match, thus skewing the proportions of B. floridae hits. We used using a custom script ("C2H2.pl" available at http://www.extavourlab.com/protocols/bio_tools/Perl_Transcriptome_Analysis_Scripts.zip) and removed reads with matches. The remaining reads were assembled with Newbler v2.5, and the resulting assembly was scanned again for the presence of C2H2 Zn finger-encoding sequences; assembled reads with hits were discarded. The remaining sequences were compared with nr using BLAST.
Estimating sequencing depth and transcript completion
To determine to what extent we had saturated gene discovery in the libraries we sequenced, we performed independent assemblies of ten progressively larger, randomly sampled subsets of the reads. The total number of genes in each sub-assembly was then identified via BLASTX against nr. If multiple isotigs or contigs hit non-overlapping portions of the same top BLAST hit, only one of these sequences was counted. To calculate the ortholog hit ratio , we first used the script for generating a list of unique BLAST results described above ("UniqueBlast.pl"). We then used a custom ortholog hit ratio script ("OrthologHitRatio.pl" available at http://www.extavourlab.com/protocols/bio_tools/Perl_Transcriptome_Analysis_Scripts.zip) to calculate the values used to create the graphs in Figure 6.
Estimating extent of gene family expansion
We first identified the D. pulex transcripts belonging to the duplicated gene families described by Colbourne and colleagues et al (Figure S31 in ) based on the KEGG enzyme code. We recorded the NCBI Gnomon transcript prediction ID of each D. pulex transcript that was listed with the chosen KEGG enzyme codes. We then mapped all of the P. hawaiensis isotigs against the D. pulex Gnomon-predicted transcriptome using TBLASTN. All P. hawaiensis isotigs with a top BLAST hit matching any recorded D. pulex NCBI Gnomon transcript prediction ID were identified. If the P. hawaiensis isotigs identified in this way belonged to the same isogroup, only a single isotig from that isogroup was counted. Using this method, we counted the putative number of P. hawaiensis paralogues from a chosen gene family.
[The sequence data from this study have been submitted to GenBank under study accession number SRA021010. Custom scripts generated are available at http://www.extavourlab.com/protocols/bio_tools/Python%20Transcriptome%20Analysis%20Tools.tar.gzand http://www.extavourlab.com/protocols/bio_tools/Perl_Transcriptome_Analysis_Scripts.zip. Assembly results are available at http://www.extavourlab.com/resources/index.html and at http://www.bio.miami.edu/wbrowne/BrowneLab2/Community_Resources.html.]
Thanks to Friedemann Linsler for assistance with embryo collection, Lisa Bukovnik for her administration of the sequencing, Ana Conesa and Stefan Götz for valuable comments regarding use of the Blast2GO tool, and the Extavour lab for discussions of the results. This work was partially supported by NSF grant IOS-0817678, Ellison Medical Foundation New Scholar Award AG-NS-07010-10, Harvard Stem Cell Institute Seed Grant SG-0057-10-00 (VZ) and a Milton Fund Grant (FA) to CE, an NSF Predoctoral Fellowship to BEC, and funding from the University of Miami College of Arts and Sciences to WEB.
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