A chelicerate-specific burst of nonclassical Dscam diversity
BMC Genomics volume 19, Article number: 66 (2018)
The immunoglobulin (Ig) superfamily receptor Down syndrome cell adhesion molecule (Dscam) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for both nervous and immune systems in insects. However, further information is required to develop a comprehensive view of Dscam diversification across the broad spectrum of Chelicerata clades, a basal branch of arthropods and the second largest group of terrestrial animals.
In this study, a genome-wide comprehensive analysis of Dscam genes across Chelicerata species revealed a burst of nonclassical Dscams, categorised into four types—mDscam, sDscamα, sDscamβ, and sDscamγ—based on their size and structure. Although the mDscam gene class includes the highest number of Dscam genes, the sDscam genes utilise alternative promoters to expand protein diversity. Furthermore, we indicated that the 5′ cassette duplicate is inversely correlated with the sDscam gene duplicate. We showed differential and sDscam- biased expression of nonclassical Dscam isoforms. Thus, the Dscam isoform repertoire across Chelicerata is entirely dominated by the number and expression levels of nonclassical Dscams. Taken together, these data show that Chelicerata evolved a large conserved and lineage-specific repertoire of nonclassical Dscams.
This study showed that arthropods have a large diversified Chelicerata-specific repertoire of nonclassical Dscam isoforms, which are structurally and mechanistically distinct from those of insects. These findings provide a global framework for the evolution of Dscam diversity in arthropods and offer mechanistic insights into the diversification of the clade-specific Ig superfamily repertoire.
Alternative splicing plays an important role in the generation of proteomic diversity and genomic evolution in metazoans [1, 2]. For example, the Down syndrome cell adhesion molecule (Dscam) gene in Drosophila melanogaster has the potential to generate 38,016 distinct mRNA and protein isoforms via mutually exclusive alternative splicing . In this Dscam gene structure, 95 alternatively spliced exons are organised into exon 4, 6, 9, and 17 clusters that contain 12, 48, 33, and 2 copies, respectively. Forward genetic screening and biochemical approaches have shown that this extensive diversity of Dscam encoded by a single locus is required for both nervous and immune systems. Dscam isoform diversity plays an important role in neuronal wiring and self-recognition, and the extensive diversity of Dscam isoforms has been shown to confer specificity for antigen recognition [4,5,6,7,8,9,10,11,12,13].
Vertebrate Dscams, which lack the striking diversity of their insect counterparts, are involved mainly in the developmental processes of the nervous system . Interestingly, cadherin superfamily members, protocadherins (Pcdhs), might serve an analogous function in vertebrates [15,16,17]. Human Pcdh genes are arranged tandemly in three groups called Pcdhα, Pcdhβ, and Pcdhγ, with 14, 22, and 22 repeats in their respective 5′ variable regions . Unlike Drosophila Dscam1, these Pcdhs utilise alternative promoters to generate isoform diversity [19, 20]. For both Dscams and Pcdhs, isoform expression appears largely stochastic and combinatorial rather than determinative, endowing a unique cell-surface identity for each neuron [15, 16, 21, 22]. Both molecules exhibit isoform-specific homophilic binding, and they may have similar roles in the nervous system. Interestingly, Drosophila lacks the counterparts of vertebrate Pcdhs. Thus, these two phyla appear to have independently evolved similar molecular strategies for comparable roles by recruiting various molecules from different protein families .
As Pcdh isoform diversity is restricted to vertebrates, Dscam isoform diversity has been considered unique to arthropods [23, 24]. However, compared with the well-known phylogenetic distribution of vertebrate Pcdhs, Dscam diversification has not been studied in detail in arthropods, particularly in Chelicerata members, which represent a basal branch of arthropods and form the second largest group of terrestrial animals. It is generally recognised that Dscam protein structure is conserved across bilaterians, containing 10 immunoglobulin (Ig) domains and six fibronectin III (FNIII) repeats, with the tenth Ig domain located between FNIII 4 and FNIII 5 [14, 15, 17]. Recently, structural variants of Dscam have been found in Ixodes scapularis . We identified shortened Dscam genes with tandemly arrayed 5′ cassettes in several Chelicerata species, similar to vertebrate clustered Pcdhs . These results suggest that the structural and expansion pathways of Dscam might be diversified in Chelicerata species. However, no comprehensive view exists of Dscam diversification across the broad spectrum of Chelicerata. The rapidly increasing availability of genomic information regarding Chelicerata, particularly key clades such as the Xiphosuran horseshoe crab, will increase our understanding of Dscam diversification.
In this study, we performed a genome-wide comprehensive analysis of Dscam genes in chelicerates, which diverged from other Arthropod lineages ~500 million years ago. The identified Dscam genes could be grouped into one classical (LDscam) and four nonclassical (mDscam, sDscamα, sDscamβ, and sDscamγ) types based on their size and structure. Although the mDscam gene class includes the highest number of Dscam genes, the sDscam genes utilise alternative promoters to expand protein diversity. Collectively, these results demonstrate that Chelicerata specifically evolved different organisation and mechanisms that generated a diverse lineage-specific repertoire of Dscam isoforms. These findings highlight the rich Chelicerata-specific diversification of Dscam genes, and provide a global framework for the evolution of Dscam diversity in arthropods and bilaterians.
Genome-wide identification of Dscam genes across Chelicerata species
To generate a global blueprint for Dscam diversity in Chelicerata, we performed a genome-wide analysis of Dscam homologues in representative species from each of the major clades. We examined one species of the order Xiphosura (Limulus polyphemus) and five species representing five major clades of the class Arachnida, including two Araneae (Stegodyphus mimosarum and Parasteatoda tepidariorum), one Scorpiones (Mesobuthus martensii), one Mesostigmatan (Metaseiulus occidentalis), and one Ixodidan (Ixodes scapularis) (Additional file 1: Table S1). These organisms constitute some of the major taxonomic groups of the Chelicerata subphylum that last shared a common ancestor ~500 million years ago , with long-term resolution (comparing the gene organisation among the five Arachnida clades and Merostomata). Using cross-species comparisons with RNA-sequencing (RNA-seq) analyses, we identified 198 Dscam genes in six representatives of the Chelicerata species, 161 of which were novel or corrected (Fig. 1b; Additional file 2: Table S2). Our results indicated that all extant chelicerates display marked expansion of the Dscam gene family.
Phylogenetic analysis indicated that all of the Dscam proteins could be clustered into three groups: canonical Dscams and two groups of shortened nonclassical proteins (Fig. 2). The three groups differ in size, and are hereafter referred to as LDscam, mDscam, and sDscam, respectively (Fig. 1a). The sDscams lack the canonical Ig1–6,10 and FNIII 3–4,6 domains present in classical Dscam. The genes encoding these sDscams can be subdivided into three types—sDscamα, sDscamβ, and sDscamγ—based on differing structures in the 5′ regions (Fig. 1a). sDscamα and sDscamβ are characterised by clustered cassette repeats in the 5′ regions, encoding one and two Ig domains, respectively. sDscamγ shares similar domains with sDscamα and sDscamβ, albeit without tandemly arrayed cassettes in the 5′ regions. Another type of shortened Dscam lacks the FNIII and Ig domains present in the C-terminal region of classical Dscam. As the sizes of these Dscams fall between those of canonical Dscam (LDscam) and sDscam, we designated these intermediate shortened Dscam genes as mDscams. As shown in Fig. 1b, nonclassical Dscams dominate the isoform repertoire in all Chelicerata species investigated.
Nonclassical Dscam genes are Chelicerata-conserved and restricted
This study revealed that nonclassical Dscams are conserved across Chelicerata species and that all types of sDscams (sDscamα, sDscamβ, and sDscamγ) are largely present in representative species from the Arachnida and Merostomata classes investigated in this study (Fig. 1b). Our results suggest that these types of nonclassical Dscams are ancient, existing before the split of Arachnida and Merostomata. The Dscam gene family members diverged markedly across various species. The higher gene number in scorpions, spiders, and horseshoe crabs is consistent with an additional event of whole or large-scale genomic duplications . Although mDscam genes are present in greater numbers than LDscams and sDscams, the sDscam genes can generate up to a hundred isoforms through a combination of alternating promoters and alternative splicing. Thus, based on the isoform number, sDscams are represented more than LDscams and mDscams in each Chelicerata. However, no such nonclassical Dscams have been identified among the Dscam genes from the Mandibulata species of insect, Crustacea, or Myriapoda classes, or in any non-arthropod species. This observation suggests that they arose after the radiation of Mandibulata and Chelicerata during Arthropoda evolution. Thus, we conclude that the nonclassical Dscams are largely conserved and restricted to Chelicerata.
Global analysis of Dscam relationships over the Chelicerata phylogeny
To trace the evolutionary history of nonclassical Dscam genes, we first performed multiple sequence alignments of all Dscams from six representative species. Comparative analysis of Dscam sequences from Chelicerata and outgroup species revealed three major clades, which represent three groups of LDscam, mDscam, and sDscam (Fig. 2). Based on the phylogenies of individual Dscam types (Additional file 3: Figures S1 and S2), although our analyses of the Dscam genes did not permit a full ancestral reconstruction, several conclusions could be reached. First, these data indicate that at least seven mDscams and five sDscams were present in the Chelicerata ancestor before the split of Arachnida and Merostomata (Additional file 3: Figures S1 and S2). Second, three types of LDscams, mDscams, and sDscams were inconsistently expanded. mDscam genes have undergone massive duplications during Chelicerata evolution, while LDscam genes have undergone few or limited duplications (Fig. 2; Additional file 3: Figures S1 and S2). For example, the divergence of the Araneae ancestor into the P. tepidariorum and S. mimosarum ancestors involved 10 P. tepidariorum-specific duplications of mDscam (Additional file 3: Figure S1). This gene expansion process is ongoing, as demonstrated by recent duplications in the Araneae species.
Phylogenetic analysis revealed that sDscams could be clustered into four clades (clades A−D; Additional file 3: Figure S2). Clade D exclusively included sDscamβs from all species investigated, suggesting this sDscamβ is ancient and arose in the Chelicerata ancestor. Clade B consisted of conserved sDscamαs and species-specific sDscamγ, suggesting that this sDscamα arose from the Chelicerata ancestor. Interestingly, clade C included species-specific sDscamβs and sDscamαs, in addition to sDscamγs. We speculate that an sDscamγ ancestor evolved differentially into sDscamβs or sDscamαs during Chelicerata divergence. These results indicated that sDscamβs and sDscamαs might have multiple independent origins.
A lineage-specific burst of 5′ clustered cassettes in sDscam genes
To produce an overview of the evolutionary relationships among the variable cassettes, we generated heatmaps for sDscamα and sDscamβ to show the relative similarities of each cassette repeat to other variable repeats both within and between species. For these analyses, we selected one representative species from each of the major orders investigated: M. occidentalis, S. mimosarum, M. martensii, I. scapularis, and L. polyphemus. Analysis of the heatmaps of the tandemly arrayed 5′ cassettes in the sDscamαs and sDscamβs revealed little evidence of conserved orthologous pairs of repeats between species (Fig. 3a, b). Instead, when striking similarities were found between repeats in each species, they typically involved large blocks of highly similar cassettes within each gene of one species. For example, a massive block of 62, 36, and 18 cassettes expanded specifically in sDscamα of M. occidentalis, and in sDscamα1 and sDscamα2 of S. mimosarum, respectively (Fig. 3c). Similarly, blocks of 21 and 33 cassettes in the M. occidentalis sDscamβ1 and sDscamβ2, respectively, were highly similar to one another (Fig. 3b, d). Phylogenetic analysis of duplicated cassettes from two closely related spiders (S. mimosarum and P. tepidariorum) indicated that 5′ cassette duplication largely occurs in a lineage-specific manner (Additional file 3: Figure S3). Furthermore, duplicated cassettes showed the tendency to be located adjacent to one another within a gene. Overall, these data indicate that the main expansions of ancestral cassettes of sDscamα and sDscamβs occurred independently in each lineage.
The heatmap patterns differed considerably between sDscamαs and sDscamβs among the various species. The sDscamα heatmap revealed large blocks of cassette duplications specific to each clade, consistent with phylogenetic analyses of duplicated cassettes across Chelicerata species (Fig. 3c). In contrast, with the exceptions of M. occidentalis, most sDscamβs contain a number of common blocks that span multiple clades, as represented in green shading in Fig. 3b. Notably, duplications of 5′ cassettes in sDscamαs and sDscamβs are almost exclusively specific to M. occidentalis, showing fewer similarities with other cassettes from other species, as represented by blue blocks in the regions of the heatmap that compare two species (Fig. 3a, b). Such high species specificity of the 5′ variable cassettes suggests that sDscamαs and sDscamβs have undergone rapid expansions and divergence. Furthermore, comparison of 5′ cassette- and gene-based clustering clearly indicated that 5′ cassette duplication occurs on a much faster timescale than gene duplication (Additional file 3: Figure S4). This multi-layer expansion of sDscam diversity might help to increase the efficiency and flexibility of spatiotemporal regulation.
5′ cassette duplicate inversely correlated with sDscam gene duplicates
As gene duplications and 5′ cassette tandem duplications increased isoform diversity through the emergence of additional genomic copies, we next investigated whether or how they are related to each other as evolutionary mechanisms. We found that the number of 5′ cassette tandem duplicates correlated inversely with that of gene duplicates in the sDscamα and sDscamβ subfamily (Fig. 4a, b). Single sDscams (singletons) are likely to contain substantially more tandem cassettes in the 5′ variable region. For example, up to 62 and 40 copies reside in the 5′ variable region of sDscamα in M. occidentalis and M. martensii, respectively. Furthermore, the sDscamα subfamily (1–3 members) contains two- to four-fold more 5′ cassette duplicates per gene, which is similar to members in the larger sDscamβ subfamily (2–7 members) (Fig. 4c); we found the reverse trend in gene duplicates (Fig. 4d). Importantly, the total number of Dscam isoforms is roughly similar among various Chelicerata species (Fig. 1b). Therefore, this correlation may reflect compensatory evolution between alternative promoter and gene duplication, analogous to the inverse correlation of alternative splicing with gene duplication . These results imply that the inverse correlation is not simply an inherent inclination, but is instead fulfilling the complementary demand for expanding Dscam isoforms via distinct evolutionary mechanisms.
To further examine the evolutionary forces underlying the inverse correlation, we carried out a detailed comparison of duplication scenarios in sDscamα and Dscamβ genes from various species. Interestingly, the number of 5′ cassette tandem duplicates per gene correlated inversely with the size of the duplicate blocks in M. occidentalis, I. scapularis, M. martensii, and S. mimosarum (Fig. 4e−h). These correlations largely fitted to a power law. L. polyphemus did not exhibit as strong a correlation as the other species (Fig. 4i), possibly due to the incomplete annotation of the Dscam genes. Furthermore, the numbers of 5′ cassette duplicates per sDscamα were roughly 1–3-fold higher than those in sDscamβs, with the duplicate blocks containing two additional exons than those in sDscamαs (Fig. 4j). This inverse relationship might reflect an inherent property of the species, i.e., the genome size (Fig. 4k, l). For example, I. scapularis, with a large genome size estimated at 2100 Mb , contained more sDscam gene duplicates, but fewer 5′ cassette tandem duplicates in each gene. In contrast, M. occidentalis, with a small genome size (~152 Mb), had fewer sDscam gene duplicates, but more 5′ cassette tandem duplicates per gene. In particular, phylogenetic analysis indicated loss of cassette-within introns occurred independently in sDscamβ1 and sDscamβ2 of M. occidentalis, whereas no substantial intron loss occurred in the constant region (Fig. 4m). This result led us to speculate that intron loss caused the decreased repeat block size to facilitate greater duplication in the 5′ variable region. Conversely, this species-specific intron loss might be driven by the selection pressure of greater cassette duplication. These results suggest that gene duplications and 5′ cassette tandem duplication are not selected to expand independently of each other during Chelicerata evolution.
Differential and biased expression of nonclassical Dscam isoforms
To further characterise the expression of nonclassical Dscam isoforms, we employed RNA-seq data to analyse the expression of the nonclassical Dscams in various tissues of M. martensii. Similar to sDscamα and sDscamβ , as well as three classical Dscams (LDscams1–3), 14 of 17 mDscams and 3 of 4 sDscamγs were expressed at markedly higher levels in the cephalothorax than in other tissues (Fig. 5a; Additional file 3: Figure S5). This expression pattern is largely coincident with high expression of classical Dscams in the nervous system of vertebrates and insects [5, 30,31,32]. In contrast, LDscams, mDscams, and sDscams showed low expression in muscles. Notably, mDscam8 was specifically expressed at maximum levels in haemocytes, whereas mDscam10 and mDscam15 were highly expressed in poison glands (Fig. 5a). It will be interesting to see whether nonclassical Dscams play a potential role in Scorpione immunity, similar to that of Dscam1 isoforms in the Drosophila immune system . These results suggest that nonclassical Dscam expression is regulated spatially and temporally.
The wealth of published RNA-seq data from a set of 20 embryo-derived cell lines allows the comparison of Dscam expression in various cell lines of I. scapularis (Additional file 4: Table S3). Expression profiling revealed that Dscam genes were differentially expressed in various cell lines (Fig. 5b). Interestingly, many Dscams were preferentially and specifically expressed in certain lines. For example, high expression of mDscam14 was observed in strain IDE2, but was almost undetectable in strain IDE8 and ISE18. In contrast, sDscamγ4 showed robust expression in strain IDE8 and ISE18, but low level expression in strain IDE12; sDscamβ2 showed high expression in strain ISE18. Likewise, the 5′ variable exons of sDscamα and sDscamβ genes exhibited differential expression in various lineages (Additional file 3: Figure S6). sDscamα2.14 was specifically expressed at maximum levels in strain ISE6, while sDscamβ2.12 and sDscamβ6.6 were expressed at maximum levels in strain ISE18 and IDE12, respectively. Collectively, these results revealed lineage-specific expression signatures of Dscam isoforms.
We observed a dramatic bias: sDscams were largely expressed at higher levels than LDscams and mDscams in various tissues of M. martensii (Fig. 6a), and in different I. scapularis lineages (Fig. 6b). A similar bias was observed in S. mimosarum, P. tepidariorum, M. occidentalis, and L. polyphemus (Fig. 6c). These data indicate that sDscam-biased expression patterns are evolutionally conserved across Chelicerata. It is possible that the high expression of sDscams might be due to the use of multiple promoters, leading to more transcripts. Taken together, both the number and expression level of nonclassical Dscams dominate exclusively in the Dscam isoform repertoire across Chelicerata.
The evolutionary landscape of Dscam diversity in arthropods
This study identified large and diverse nonclassical Dscam repertoires in chelicerates, most of which are newly annotated or corrected. The results reported here extend our previous insights into Dscam diversity during arthropod evolution [23,24,25]. Firstly, the nonclassical Dscam genes can be classified into four types (mDscam, sDscamα, sDscamβ, and sDscamγ) based on their size and structure (Fig. 1). Moreover, the nonclassical Dscam genes are conserved and restricted to Chelicerata, suggesting that Chelicerata uniquely evolved a large lineage-specific repertoire of nonclassical Dscam isoforms. Phylogenetic analysis and comparison of Dscam structures revealed that the Dscam ancestor underwent multiple shortening events during chelicerate evolution, leading to the loss of protein domains to varying degrees . Thus, the Dscam gene number has undergone massive expansion, and also the structure of Dscam genes became highly diversified during Chelicerata evolution. These findings, together with those of others [23,24,25], provide a global framework for the evolution of Dscam diversity in arthropods.
These Dscam diversifications suggest that their binding mechanisms are potentially different from those of classical Dscams. The crystal structural analysis reveals that the first four Ig domains of Drosophila Dscam1 are responsible for the formation of the horseshoe configuration . Additional modelling studies illuminated the molecular basis of the isoform-specific homophilic binding specificity . As they contain the same eight N-terminal Ig domains as Drosophila Dscam1, it is conceivable that the chelicerate mDscams studied in this research could form a horseshoe configuration and interact via a similar mechanism. However, this horseshoe structure does not form in chelicerate sDscams with only three Ig domains. Therefore, we speculate that chelicerate sDscams exhibit a different mode of isoform-specific homophilic binding than Drosophila Dscam1.
Chelicerata seem to have generated far fewer Dscam isoforms than insects. As estimated by the number of Ig7 or orthologues, the number of Dscam isoforms is in the range of ~100–200 across the Chelicerata species investigated (Fig. 1), approximately two to three orders of magnitude lower than that in insects. Recent studies indicate that clustered mammalian Pcdhs could expand the binding specificity repertoire via cis-multimers. For 22 γ-Pcdhs, the diversity of adhesive interfaces could be on the order of 105 through cis-tetramerisation coupled with homophilic trans interactions [34, 35]. Given the striking organisational resemblance between the Chelicerata clustered sDscams and mammalian Pcdhs, it is attractive to speculate that Chelicerata sDscams could function via cis-multimers. If so, the diversity of adhesive interfaces mediated by Chelicerata sDscams will be much higher, as there are many more Chelicerata-clustered sDscams (90–130) than mammalian-clustered Pcdhs (50–60).
Dscams versus Protocadherins
Dscams and Pcdhs belong to large established families of cell adhesion molecules: Dscams belong to the Ig superfamily and Pcdhs belong to the cadherin superfamily . The clustered Pcdh diversity is confined within the clade of jawed vertebrates, which is considered as a chordate innovation , whereas extensive Dscam diversity is unique to arthropods. In the latter case, arthropods diversify using two mechanisms to generate Dscam isoform diversity: Mandibulata Dscam genes employ exclusive splicing of internal exon clusters to generate distinct isoforms [3, 24] and chelicerate Dscams utilise alternative promoters in the 5′ variable region . However, neither cadherin nor protocadherin genes appear to have internal tandem exon arrays in a manner similar to Mandibulata Dscams.
Both clustered chelicerate Dscams and vertebrate Pcdhs are organised in a tandem array in the 5′ variable region (Fig. 7a, b). Curiously, both 5′ clustered sDscams and Pcdhs appeared to originate via an analogous evolutionary pathway (Fig. 7c, d), which was involved in the shortening and expansion of Dscam and cadherin ancestors [25, 38]. In both genes, each variable repeat is preceded by a promoter, and differential expression occurs via combining alternate promoter choice with alternative splicing [19, 20, 25]. Moreover, 5′ clustered Dscams and Pcdhs contain similar structural composition encoding six extracellular domains, a single transmembrane (TM) region, and a cytoplasmic domain. Interestingly, three-dimensional protein structure modelling revealed a similar β sandwich structure between the first domain of Pcdh and sDscam (Fig. 7a, b). Finally, we showed that clustered sDscams encode proteins exhibiting isoform-specific homophilic binding in a manner similar to Pcdhs. Despite their overall similarities, the structural properties of Pcdh and sDscam genes differ in at least two major aspects. First, inconsistent with the conserved arrangement of a single genome locus containing three tandem Pcdh gene clusters across vertebrates, the sDscams are largely dispersed or partially clustered in the chelicerate genome. As the transcription of Pcdh gene clusters is closely linked and mediated by long-range chromatin-looping interactions , the dispersed distribution of sDscam gene clusters might reflect a mode of transcription regulation distinct from that of Pcdh genes. A second major difference concerns the structure of the variable region. Pcdh variable exons encode the entire ectodomain composed of six extracellular cadherin domains (EC1–EC6), a single TM region, and a short cytoplasmic extension, whereas the variable cassettes of sDscams encode the partial ectodomain of one or two Ig domains at the N-terminus. Future studies are needed to investigate the role of variable region structures in the subcellular distribution, isoform-specific binding, and multimer formation.
Combining experimental evidence with the complementary phylogenetic distribution of Dscam diversity in arthropods and Pcdh diversity in vertebrates, it is tempting to suggest that both may have similar roles in the nervous system [15,16,17, 21, 22]. These two phyla seem to employ a similar strategy for self/non-self discrimination by recruiting various molecules of different protein families . Nevertheless, there is a wide evolutionary gap between arthropods and vertebrates, as they share a common ancestor more than 500 million years ago. It will be informative to explore the molecules or mechanisms of species within this phylogenetic gap (i.e., Branchiostoma floridae), which are thought to lack both clustered Pcdh and Dscam genes, and that have evolved to endow cells with distinct molecular identities and highly diverse recognition selectivity strategies.
Diversification of Ig superfamily protein repertoires
Although tandemly arrayed Ig repeats are found frequently in the genome, animals achieve protein diversity from a single locus via a variety of mechanisms (Additional file 3: Figure S7). In higher vertebrates, the great diversity of antigen-specific receptors of the adaptive immune system can be achieved through somatic gene rearrangement and clonal selection at the DNA transcriptional level, which is known as the V(D)J mechanism [40,41,42,43]. However, insect Dscam1s utilise mutually exclusive splicing to generate an extensive repertoire of thousands of Ig-superfamily protein isoforms [3, 5]. In contrast, our studies indicate that Chelicerata sDscams employ alternative promoters to generate substantial numbers of isoforms . These molecular processes are mutually exclusive among three distinct clades, functioning to create extensive molecule diversity. Metazoans might have evolved different ways for extensive Ig-superfamily proteins to enable immune defence and other functions.
In this study, we identified large and lineage-specific nonclassical Dscam repertoires in chelicerates. Nonclassical Dscams are conserved and restricted to Chelicerata, and have been classified into four types based on their size and structure. These results demonstrate that arthropods specifically diversify a large Chelicerata-specific repertoire of nonclassical Dscam isoforms. The Dscam isoform repertoire across Chelicerata is dominated exclusively by the number and expression levels of nonclassical Dscams. This genome-wide identification and classification study of Dscam genes provides the global framework of the evolution of Dscam diversity in arthropods, and provides mechanistic insights into the diversification of the species-specific Ig superfamily repertoire.
Data availability and RNA-seq data analysis
We investigated the following representative Chelicerate species: Mesostigmatan M. occidentalis, Trombidiformes I. scapularis , two Araneae S. mimosarum and P. tepidariorum , two Scorpiones M. martensii , and Merostomatan L. polyphemus. The sources of the Chelicerata genome sequences used in this study are shown in Additional file 1: Table S1. To validate the Dscam candidates, we selected 125 publically available RNA-seq datasets corresponding to various developmental stages, tissues, organs, and cell lines across six chelicerate species (Additional file 4: Table S3). All of the raw RNA-seq datasets were subject to pre-treatment, including adapter trimming and low-quality read removal using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Then, for each sequencing dataset, the count of each RNA-seq read was normalized to reads per million (RPM), thus enabling cross-sample comparison of the Dscam expression levels. Specifically, to calculate the RPM of one RNA-seq read, the raw count of the read was divided by the total raw count of the RNA-seq dataset and multiplied by 106. The treated reads were mapped onto the transcripts using Bowtie 2 . From these mappings, we were able to calculate the expression levels in reads per kilobase of transcript per million mapped reads (RPKM).
Availability of genome and RNA-seq data
We investigated the following representative species of Chelicerate: Mesostigmatan M. occidentalis, Trombidiformes I. scapularis , two Araneae S. mimosarum and P. tepidariorum , two Scorpiones M. martensii , and Merostomatan L. polyphemus. The sources of the Chelicerata genome sequences used in this study are shown in Additional file 1: Table S1. For Dscam candidate validation, we selected 125 publically available RNA-seq data corresponding to various developmental stages, tissues, and organs, and cell lines across six chelicerate species (Additional file 4: Table S3).
Annotation and identification of Dscam genes
The sequences of the Dscam homologues were annotated through cross-species BLAST searches using the available annotated Dscam sequences (http://blast.ncbi.nlm.nih.gov/Blast.cgi). These Dscam candidate homologues were validated further using publically available transcriptome and RNA-seq datasets. All Dscam candidates were confirmed by phylogenetic analysis (http://www.ebi.ac.uk/clustalw/index.html) and then analysed by classifying and predicting protein domains with InterPro  (http://www.ebi.ac.uk/interpro/) and PROSITE  (http://prosite.expasy.org/prosite.html). The Dscam genes identified in representative species of Chelicerate are listed in Additional file 2: Table S2.
The Dscam sequences were aligned across species using the Clustal W2 software package (http://www.ebi.ac.uk/clustalw/index.html) . The coding sequences of the variable region were translated, and the resulting polypeptides were aligned. The nucleotide sequences of each 5′ variable cassette of sDscam were translated into amino acid sequences and aligned. The genetic distances for each gene were estimated using MEGA 7.0 software . We used maximum likelihood (ML) methods, using MEGA , to build the phylogenies. For the ML analysis, we ran MEGA with at least 1000 bootstrap replicates. To determine the homology of the Dscam-related genes found in metazoans, we estimated the phylogenies of 217 proteins, including Dscams encompassing the seventh Ig domains to the end (sDscam regions encompassing the first Ig domains to end) (Fig. 2). This phylogeny was rooted using the sequence of the Nematostella vectensis Dscam (GenBank:ABAV01020293.1) . We used the duplicated cassettes encoding the Ig1 domain of sDscamα to dissect the evolutionary relationships between the duplicated cassettes with a tree rooted on the D. melanogaster Dscam1 duplicated exon 9.1, which encodes the Ig7 domain (Additional file 3: Figure S3a). Similarly, we used the duplicated cassettes, which encode the Ig1 + 2 domain of sDscamβ and a tree rooted on the D. melanogaster Dscam1 exon 9.1, 10, and 11, which encode the Ig7 + 8 domains (Additional file 3: Figure S3b).
Protein three-dimensional structure modelling
All three-dimensional proteins structures were acquired using the Swiss-Model (automated mode) (www.swissmodel.expasy.org). The structures were displayed and processed using the PyMOL software package (www.pymol.com).
Analysis of differential and biased expression
The RNA-seq data from publically available samples were used to analyse the expression of nonclassical Dscam genes at various developmental stages, tissues types, and cell lines (Additional file 4: Table S3). For each sample, we calculated the RPKM value of the constant exonic region to measure the expression level of each Dscam gene from the replicates. The alternative exon encoding Ig7 was selected to calculate the expression level from the replicates for each 5′ variable cassette. Considering the short length of the alternative exons, the RNA-seq reads were split into 25-nucleotide (nt) fragments for mapping by using Bowtie 2 software , and only the perfectly mapped fragments were retained for expression level calculation. Furthermore, the read counts of a 25-nt fragment with multiple loci were divided by the number of loci, and then assigned equally to each locus for expression level calculation. To eliminate influences on calculations of the expression levels from identical sequences among exon duplicates, both the 25-nt fragments and the full-length RNA-seq reads (150 nt) were used to calculate the expression profiles as previously described . If, as a result of originating from a repetitive region, one RNA-seq read or fragment mapped onto several loci, we divided the RPM value of this RNA-seq read by the number of repetitive loci, then evenly assigned it to each transcript in the expression level calculation.
We used an independent sample t-test to assess the relationship between the 5′ cassette duplicate and the sDscam gene duplicate. We compared the numbers of 5′ cassettes and gene duplicates between the sDscamα and sDscamβ groups using a two-tailed Student’s t-test. We defined correlation and significance levels for the number of 5′ cassette duplicates and the repeat size in terms of a simple regression model. We also used a two-tailed Student’s t-test to compare the differences between the expression levels in groups of mDscams and sDscams across various species. Effects were considered to be statistically significant when p < 0.05.
Basic local alignment search tool
Down syndrome cell adhesion molecule
Extracellular cadherin domains
Molecular evolutionary genetics analysis
Reads per kilobase of transcript per million mapped reads
Reads per million
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We thank Dr. Qi Zhou, Institute of Life Sciences, Zhejiang University, China, for the critical reading of the manuscript.
This work was supported by research grants from the National Natural Science Foundation of China (31630089, 31430050, 91740104).
Availability of data and materials
All data generated or analysed during this study are included in this published article and its Additional files. The Dscam gene sequences were deposited into GenBank with accession numbers: MF106020−MF106053; MF066898−MF066905; KX555546−KX555560; KU641421− KU641424.
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Chelicerata species and their genome sources in this study. (XLSX 10 kb)
A list of Dscam homologues identified in Chelicerata species. (XLSX 25 kb)
Supplementary Figures S1–S7. (PDF 1532 kb)
RNA-seq datasets in Chelicerata species. (XLSX 21 kb)
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Cao, G., Shi, Y., Zhang, J. et al. A chelicerate-specific burst of nonclassical Dscam diversity. BMC Genomics 19, 66 (2018). https://doi.org/10.1186/s12864-017-4420-0