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Central Nervous System Transcriptome of Biomphalaria Alexandrina, an Intermediate Host for Schistosomiasis Tamer A

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Central Nervous System Transcriptome of Biomphalaria Alexandrina, an Intermediate Host for Schistosomiasis Tamer A Mansour et al. BMC Res Notes (2017) 10:729 https://doi.org/10.1186/s13104-017-3018-6 BMC Research Notes RESEARCH NOTE Open Access Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis Tamer A. Mansour1,2, Mohamed R. Habib3, Laura C. Vicente Rodríguez4, Anthony Hernández Vázquez4, Julián Maldonado Alers4, Alfredo Ghezzi5, Roger P. Croll6, C. Titus Brown1 and Mark W. Miller4* Abstract Objective: Globally, more than 200 million people live at risk of the neglected tropical disease schistosomiasis (or snail fever). Larval schistosomes require the presence of specifc snail species that act as intermediate hosts, support- ing their multiplication and transformation into forms that can infect humans. This project was designed to generate a transcriptome from the central nervous system (CNS) of Biomphalaria alexandrina, the major intermediate host for Schistosoma mansoni in Egypt. Results: A transcriptome was generated from fve pooled central nervous systems dissected from uninfected specimens of B. alexandrina. Raw Illumina RNA-seq data (~ 20.3 million paired end reads of 150 base pairs length each) generated a transcriptome consisting of 144,213 transcript elements with an N50 contig size of 716 base pairs. Orthologs of 15,246 transcripts and homologs for an additional 16,810 transcripts were identifed in the UniProtKB/ Swiss-Prot database. The B. alexandrina CNS transcriptome provides a resource for future research exploring parasite- host interactions in a simpler nervous system. Moreover, increased understanding of the neural signaling mechanisms involved in the response of B. alexandrina to infection by S. mansoni larvae could lead to novel and highly specifc strategies for the control of snail populations. Keywords: Biomphalaria alexandrina, Schistosoma mansoni, CNS, Trematode, Gastropod, Mollusk, Nile Introduction Fresh water pulmonate snails from the genus Biom- Schistosomiasis remains one of the most prevalent phalaria act as the obligatory intermediate host for neglected tropical diseases afecting human popula- Schistosoma mansoni, the trematode species that causes tions in many parts of Africa, Asia, and South America. intestinal schistosomiasis. A recent whole genome anal- Te World Health Organization (WHO) estimated that ysis for Biomphalaria glabrata, the major intermedi- more than 218 million people in 78 countries required ate host in the Western Hemisphere, identifed several preventive chemotherapy in 2015 [1]. Te WHO has potential targets for developing novel control measures recommended a multifaceted strategic plan for control [3]. In Egypt, where schistosomiasis dates to antiquity and prevention of schistosomiasis, including large-scale [4–6], Biomphalaria alexandrina is the predominant chemotherapy for high-risk populations, hygiene educa- intermediate host for S. mansoni [7–9]. Te presence of tion, access to safe drinking water, and snail control [2]. B. alexandrina is a key factor that determines the preva- lence of intestinal schistosomiasis in the country. In 2016, the Ministry of Health and Population of Egypt *Correspondence: [email protected] (MoHP) and WHO conducted a mapping of S. mansoni 4 Institute of Neurobiology and Department of Anatomy & Neurobiology, infection in fve Nile Delta governorates [10]. Te results University of Puerto Rico, Medical Sciences Campus, 201 Blvd del Valle, of this project showed that prevalence rates ranged San Juan, Puerto Rico Full list of author information is available at the end of the article from 4.7% in Qalyubia Governorate to 17.6% in Sharqia © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Mansour et al. BMC Res Notes (2017) 10:729 Page 2 of 6 Governorate, with an average prevalence of 10.7% in the nervous systems (Fig. 1b) were dissected, immediately fve governorates surveyed. Tese observations indicate submerged in RNAlater (Termo Fisher Scientifc, USA), that previous assessments may have underestimated the and stored at 4 °C for further analysis. Five pooled nerv- extent of infection. ous systems were homogenized in lysis-binding solution Eforts to control snail populations, such as mollusci- provided in the RNAqueous-Micro Total RNA Isolation cides or introduction of predator species, have yielded Kit (Termo Fisher Scientifc, USA). Total RNA was iso- only modest results. One potential target to be consid- lated following the manufacturer’s instructions. Te RNA ered for snail control is its central nervous system (CNS), was quantifed using a NanoDrop spectrophotometer since it regulates vital functions including cardiac activ- and its quality was verifed with an agarose gel. Samples ity, feeding and reproductive behavior. In the present were then sent to the Genomic Sequencing and Analysis investigation, a neural transcriptome was generated with Facility (GSAF) at the University of Texas at Austin for the ultimate goal of identifying signaling mechanisms library preparation and Illumina sequencing. PolyA RNA involved in the response of B. alexandrina to infection selection was implemented using the Poly(A)Purist MAG by S. mansoni larvae. Such mechanisms may lead to Kit (Life Technologies). Te mRNA quality was assessed novel and highly specifc strategies for the control of snail with an Agilent Bioanalyzer. A non-directional RNA-seq populations. library (cDNA inserts of approximately 384 bp) was gen- erated using NEBNext Module Components. Sequenc- Main text ing was performed on an Illumina HiSeq 4000 sequencer Methods (Paired End 2 × 150 bp). Sample collection and preparation Specimens of B. alexandrina (Fig. 1a) used in the present Transcriptome preprocessing, assembly and annotation study were descendants from a feld population that was Quality based trimming was implemented using Trim- collected from Giza Governorate in Egypt in 2012 and momatic v0.33 [11] followed by K-mer spectral analysis shipped to the Faculty of Medicine, Dalhousie University, to remove low abundance K-mers using the Khmer 2.0 Canada. Tey were maintained under a 14:10 light–dark package [12]. FastQC v0.11.3 was used to check data cycle and fed romaine lettuce ad libitum. Te central quality before and after trimming [13]. Filtration of input Fig. 1 Source of RNA used to generate transcriptome. a Biomphalaria alexandrina specimen. Calibration bar: 1 mm. b Dissected central nervous system. B g., buccal ganglion; C g., cerebral ganglion; V g., visceral ganglion. Calibration bar: 200 μm Mansour et al. BMC Res Notes (2017) 10:729 Page 3 of 6 sequences produced ~ 14.4 million paired end (PE) reads complete, fragmented, and missing gene models. To and ~ 5.4 million single end (SE) reads. High-quality frag- assess expression abundance of assembled transcripts, ments were pooled for de novo transcriptome assembly mapped sequence reads were normalized into transcript using Trinity v2.2.0 [14] producing 149,545 transcripts. per million scale (TPM) and logarithmic transformation Several fltration procedures were performed to clean up of the normalized expression was plotted as a histogram the assembly: SeqClean was used to trim poly-A tails and (Fig. 2). Most of the transcripts had expression abun- remove 38 low complexity sequences [15]. Custom scripts dance levels around 1.5 TPM but only 848 transcripts were used to remove 745 fragments smaller than 200 bp. had TPM values greater than 100 (Expression statistics: Back-mapping of input sequencing reads to the assembly Table 2). using Salmon software, allowed removal of 4526 uncov- For annotation, TransDecoder v2.0.1 was used to ered isoforms [16]. Finally, scanning the new assembly predict open reading frames (ORFs) [20]. A recipro- against the UniVec Database containing vector and artif- cal BLAST search was implemented between the fnal cial sequences eliminated 23 transcripts and trimmed an assembly and target databases using BLAST plus v2.2.30. additional 98 transcripts [17]. In total, all fltration steps Signifcant BLAST hits (E-values < 10e−5) were utilized excluded 5332 transcripts. Te fnal assembly was com- by crb-BLAST software to identify orthologous tran- posed of 144,213 isoforms that belong to 128,739 genes. scripts [21]. Transcripts with signifcant BLAST hits that Te total assembly size was 82.7 Mb with N50 equal to failed to fnd a signifcant ortholog were annotated by the 716 base pairs. (Assembly statistics: Table 1). To evalu- best BLAST hit as a candidate homolog. ate the quality of the fnal assembly, another round of back mapping of input sequencing reads to the assem- bly was performed. PE and SE reads showed mapping rates of about 96 and 89% respectively. For benchmark- ing, Universal Single-Copy Orthologs (BUSCO v.2) soft- ware was used to assess annotation completeness against single-copy orthologs in Metazoa (978 orthologs) [18, 19]. BUSCO analysis was able to identify 79.5, 19.5, 1.1% Table 1 Transcriptome assembly statistics Total trinity ‘genes’ 128739 Total trinity transcripts 144213 Maximum length 5634 Minimum length 201 Percent GC 36.75 Statistics based on ALL transcript contigs Contig N10 1986 Contig N20 1459 Contig N30 1128 Contig N40 896 Contig N50 716 Median contig length 402 Mean contig length 573 Fig. 2 Histogram of log TPM expression Total assembled bases 82,672,833 Statistics based on LONGEST ISOFORM per “GENE” Table 2 Expression abundance statistics Contig N10 1797 Contig N20 1298 Mean expression 6.93 Contig N30 1001 Median expression 1.47 Contig N40 796 Maximum expression 27609 Contig N50 636 Isoforms with exp > 10 TPM 11187 Median contig length 382 Isoforms with exp > 100 TPM 848 Mean contig length 533 Isoforms with exp > 1000 TPM 85 Total assembled bases 68,601,167 Isoforms with exp > 10000 TPM 3 Mansour et al.
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