The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

FishDB: an integrated functional genomics database for fishes

Background

Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data.

Results

Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb.ihb.ac.cn. The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes.

Conclusions

This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07159-9.

The Grass Carp Genomic Visualization Database (GCGVD): an informational platform for genome biology of grass carp

With the release of the draft genome of the grass carp, researches on the grass carp from the genetic level and the further molecular mechanisms of economically valuable physiological behaviors have gained great attention. In this paper, we integrated a large number of genomic, genetic and some other data resources and established a web-based grass carp genomic visualization database (GCGVD). To view these data more effectively, we visualized grass carp and zebrafish gene collinearity and genetic linkage map using Scalable Vector Graphics (SVG) format in the browser, and genomic annotations by JBrowse. Furthermore, we carried out some preliminary study on a whole-genome alternative splicing (AS)of the grass carp. The RNA-seq reads of 15 samples were aligned to the reference genome of the grass carp by Bowtie2 software. RNA-seq reads of each sample and density map of reads were also exhibited in JBrowse. Additionally, we designed a universal grass carp genome annotation data model to improve the retrieval speed and scalability. Compared with the published database GCGD previously, we newly added the visualization of some more genomic annotations, conserved domain and RNA-seq reads aligned to the reference genome. GCGVD can be accessed at http://122.112.216.104.

Ceruloplasmin, a moonlighting protein in fish

Ceruloplasmin is an ancient multicopper oxidase evolved to insure a safe handling of oxygen in some metabolic pathways of vertebrates. The current knowledge of its structure provides a glimpse of its plasticity, revealing a multitude of binding sites that point to an elaborate mechanism of multifunctional activity. Ceruloplasmin is highly conserved throughout the vertebrate evolution. Cupredoxin, a multi-cupper blue protein is believed to be the evolutionary precursor of ceruloplasmin with three trinuclear and three mononuclear copper binding sites. There are 20 copper-binding residues in ceruloplasmin gene out of which 16 residues are conserved in fish. This ceruloplasmin gene is being characterized in zebrafish (Danio rerio), rohu (Labeo rohita), Indian medaka (Oryzias melastigama), catfish (Ictalurus punctatus), icefish (Chionodraco rastrospinosus), goldfish (Carassius auratus) and yellow perch (Perca flaviscens). The complete coding sequence of fish ceruloplasmin gene is around 3.2 kb which codes for 1000 to 1100 amino acid residues. The size of ceruloplasmin gene sequence in fish ranges around 13 kb containing 20 exons and 19 introns. Liver is the major site of synthesis in fish. Increased expression of this gene during bacterial infection in channel catfish and rohu suggested its potential involvement in bacterial disease response in fish. It has been found to serve as an indirect marker for selection against Aeromonas hydrophila resistance in rohu carp. Ceruloplasmin expression is also evident during parasitic infection in few fish species. The role of this gene is well studied during inflammatory response to hormonal, drug and heavy metal mediated toxicity in fish. Overall, ceruloplasmin represents an example of a 'moonlighting' protein that overcomes the one gene-one structure-one function concept to follow the changes of the organism in its physiological and pathological conditions.

Analysis of apolipoprotein genes and their involvement in disease response of channel catfish after bacterial infection

Apolipoproteins are protein component of plasma lipoproteins. They exert crucial roles in lipoprotein metabolism and serve as enzyme cofactors, receptor ligands, and lipid transfer carriers in mammals. In teleosts, apolipoproteins are also involved in diverse processes including embryonic and ontogenic development, liver and digestive system organogenesis, and innate immunity. In this study, we identified a set of 19 apolipoprotein genes in channel catfish (Ictalurus punctatus). Phylogenetic analysis and syntenic analysis were conducted to determine their identities and evolutionary relationships. The expression signatures of apolipoproteins in channel catfish were determined in healthy tissues and after infections with two major bacterial pathogens, Edwardsiella ictaluri and Flavobacterium columnare. In healthy channel catfish, most apolipoprotein genes exhibited tissue-specific expression patterns in channel catfish. After ESC and columnaris infections, 5 and 7 apolipoprotein genes were differentially expressed respectively, which presented a pathogen-specific and time-dependent pattern of regulation. After ESC infection, three exchangeable apolipoproteins (apoA-IB, apoC-I, and apoE-B) were suppressed in catfish intestine, while two nonexchangeable apolipoproteins (apoB-A and apoB-B) were slightly up-regulated. After columnaris infection, apoB-B, apoD-B, and apoE-A were significantly down-regulated in catfish gill, while apoF, apoL-IV, apoO-like, and apo-14 kDa showed significantly up-regulation. Taken together, these results suggested that apolipoprotein genes may play significant roles in innate immune responses to bacterial pathogens in channel catfish.

Septin genes in channel catfish (Ictalurus punctatus) and their involvement in disease defense responses

Septins are an evolutionarily conserved family of GTP-binding proteins. They are involved in diverse processes including cytokinesis, apoptosis, infection, neurodegeneration and neoplasia. In this study, through thorough data mining of existed channel catfish genomic resources, we identified a complete set of 15 septin genes. Septins were classified into four subgroups according to phylogenetic analysis. Extensive comparative genomic analysis, including domain and syntenic analysis, supported their annotation and orthologies. The expression patterns of septins in channel catfish were examined in healthy tissues and after infection with two major bacterial pathogens, Edwardsiella ictaluri and Flavobacterium columnare. In healthy channel catfish, most septin genes were ubiquitously expressed and presented diversity patterns in various tissues, especially mucosal tissues, proposing the significant roles septin genes may play in maintaining homeostasis and host immune response activities. After bacterial infections, most septin genes were regulated, but opposite direction in expression profiles were found with the two bacterial pathogens: the differentially expressed septin genes were down-regulated in the intestine after E. ictaluri infection while generally up-regulated in the gill after F. columnare infection, suggesting a pathogen-specific and tissue-specific pattern of regulation. Taken together, these results suggested that septin genes may play complex and important roles in the host immune responses to bacterial pathogens in channel catfish.

Complement regulatory protein genes in channel catfish and their involvement in disease defense response

Complement system is one of the most important defense systems of innate immunity, which plays a crucial role in disease defense responses in channel catfish. However, inappropriate and excessive complement activation could lead to potential damage to the host cells. Therefore the complement system is controlled by a set of complement regulatory proteins to allow normal defensive functions, but prevent hazardous complement activation to host tissues. In this study, we identified nine complement regulatory protein genes from the channel catfish genome. Phylogenetic and syntenic analyses were conducted to determine their orthology relationships, supporting their correct annotation and potential functional inferences. The expression profiles of the complement regulatory protein genes were determined in channel catfish healthy tissues and after infection with the two main bacterial pathogens, Edwardsiella ictaluri and Flavobacterium columnare. The vast majority of complement regulatory protein genes were significantly regulated after bacterial infections, but interestingly were generally up-regulated after E. ictaluri infection while mostly down-regulated after F. columnare infection, suggesting a pathogen-specific pattern of regulation. Collectively, these findings suggested that complement regulatory protein genes may play complex roles in the host immune responses to bacterial pathogens in channel catfish.

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.

Hsp90, Hsp60 and sHsp families of heat shock protein genes in channel catfish and their expression after bacterial infections

Heat shock proteins (Hsps) are a suite of highly conserved proteins whose expressions are generally induced by elevated temperature. However, many Hsps play important roles in both innate and adaptive immunity. On the basis of our previous work on Hsp40 and Hsp70 gene families in channel catfish (Ictalurus punctatus), the objective of this study was to characterize Hsp90, Hsp60, Hsp10, and small Hsp genes, and to investigate their expression profiles after bacterial infections. A total of 20 Hsp genes were identified and annotated in the channel catfish genome, including five Hsp90 genes, one Hsp60 gene, one Hsp10 gene, and 13 sHsp genes. Six Hsp genes were differentially expressed after Edwardsiella ictaluri infection, and 12 were differentially expressed after Flavobacterium columnare infection. Although expression of these genes exhibited both temporal and spatial regulation, the induction of Hsp genes was observed soon after bacterial infection, while the suppression of Hsp genes was observed at later time-points, suggesting their distinct roles in immune responses and disease defenses. A pathogen-specific expression pattern of Hsp90 was observed. After F. columnare infection, all Hsp90 genes were found up-regulated except Hsp90ab1, which was not significantly regulated. However, after E. ictaluri infection, only one Hsp90 gene was found significantly down-regulated. Both pathogen-specific and tissue-specific pattern of expression were observed with small Hsps after E. ictaluri and F. columnare bacterial infections. These results suggested that most of Hsp genes may play important roles in immune response and/or disease defense in channel catfish.

Molecular cloning, sequencing and tissue expression of vasotocin and isotocin precursor genes from Ostariophysian catfishes: phylogeny and evolutionary considerations in teleosts

Basic and neutral neurohypophyseal (NH) nonapeptides have evolved from vasotocin (VT) by a gene duplication at the base of the gnathostome lineage. In teleosts, VT and IT are the basic and neutral peptides, respectively. In the present study, VT and IT precursor genes of Heteropneustes fossilis and Clarias batrachus (Siluriformes, Ostariophysi) were cloned and sequenced. The channel catfish Icatalurus punctatus NH precursor sequences were obtained from EST database. The catfish NH sequences were used along with the available Acanthopterygii and other vertebrate NH precursor sequences to draw phylogenetic inference on the evolutionary history of the teleost NH peptides. Synteny analysis of the NH gene loci in various teleost species was done to complement the phylogenetic analysis. In H. fossilis, the NH transcripts were also sequenced from the ovary. The cloned genes and the deduced precursor proteins showed conserved characteristics of the NH nonapeptide precursors. The genes are expressed in brain and ovary (follicular envelope) of H. fossilis with higher transcript abundance in the brain. The addition of the catfish sequences in the phylogenetic analysis revealed that the VT and IT precursors of the species-rich superorders of teleosts have a distinct phylogenetic history with the Acanthopterygii VT and IT precursors sharing a less evolutionary distance and the Ostariophysi VT and IT having a greater evolutionary distance. The genomic location of VT and IT precursors, and synteny analysis of the NH loci lend support to the phylogenetic inference and suggest a footprint of fish- specific whole genome duplication (3R) and subsequent diploidization in the NH loci. The VT and IT precursor genes are most likely lineage-specific paralogs resulting from differential losses of the 3R NH paralogs in the two superorders. The independent yet consistent retention of VT and IT in the two superorders might be directed by a stringent ligand-receptor selectivity.

Pathogen recognition receptors in channel catfish: III phylogeny and expression analysis of Toll-like receptors

Toll-like receptors (TLRs) were the earliest characterized and the most extensively studied pathogen recognition receptors (PRRs). The majority of tetrapod TLR orthologs have been found in teleost fish. In addition, a group of "fish-specific" TLRs have been identified. In catfish, a number of TLR-related sequences have been reported, but systematic phylogenetic analyses have not been conducted. In this study, we conducted phylogenetic and comparative analysis of 20 catfish TLR genes against their counterparts from various species. TLR25 and TLR26 are TLRs identified only in channel catfish. Phylogenetic analyses suggested that four catfish TLR genes have duplicated copies in the genome, i.e., TLR4, TLR5, TLR8, and TLR20. Six fish-specific TLRs were identified, and the vast majority of these belong to the TLR11 subfamily. In healthy catfish tissues, most of the tested TLR genes were ubiquitously expressed although expression levels varied among the 11 tested tissues. We tested nine TLRs for their expression in response to Edwardsiella ictaluri infection. They were significantly up-regulated in the spleen and liver, but down-regulated in the head kidney, suggesting their involvement in the immune responses against the intracellular bacterial pathogen in a tissue-specific manner in catfish, perhaps through rapid migration of phagocytes to infection sites.

A consensus linkage map provides insights on genome character and evolution in common carp (Cyprinus carpio L.)

Common carp (Cyprinus carpio L.) is cultured worldwide and is a major contributor to the world's aquaculture production. The common carp has a complex tetraploidized genome, which may historically experience additional whole genome duplication than most other Cyprinids. Fine maps for female and male carp were constructed using a mapping panel containing one F1 family with 190 progeny. A total of 1,025 polymorphic markers were used to construct genetic maps. For the female map, 559 microsatellite markers in 50 linkage groups cover 3,468 cM of the genome. For the male map, 383 markers in 49 linkage groups cover 1,811 cM of the genome. The consensus map was constructed by integrating the new map with two published linkage maps, containing 732 markers and spanning 3,278 cM in 50 linkage groups. The number of consensus linkage groups corresponds to the number of common carp chromosomes. A significant difference on sex recombinant rate was observed that the ratio of female and male recombination rates was 4.2:1. Comparative analysis was performed between linkage map of common carp and genome of zebrafish (Danio rerio), which revealed clear 2:1 relationship of common carp linkage groups and zebrafish chromosomes. The results provided evidence that common carp did experienced a specific whole genome duplication event comparing with most other Cyprinids. The consensus linkage map provides an important tool for genetic and genome study of common carp and facilitates genetic selection and breeding for common carp industry.

Identification and characterization of microRNAs in channel catfish (Ictalurus punctatus) by using Solexa sequencing technology

Channel catfish (Ictalurus spp.) is an economically important species in freshwater aquaculture around the world and occupies a prominent position in the aquaculture industry of the United States. MicroRNAs (miRNAs) play important roles in the regulation of almost every biological process in eukaryotes; however, there is little information available concerning miRNAs in channel catfish. In this study, a small-RNA cDNA library was constructed from 10 tissues of channel catfish, and Solexa sequencing technology was used to perform high-throughput sequencing of the library. A total of 14,919,026 raw reads, representing 161,288 unique sequences, were obtained from the small-cDNA library. After comparing the small RNA sequences with the RFam database, 4,542,396 reads that represent 25,538 unique sequences were mapped to the genome sequence of zebrafish to perform distribution analysis and to screen for candidate miRNA genes. Subsequent bioinformatic analysis identified 237 conserved miRNAs and 45 novel miRNAs in the channel catfish. Stem-loop RT-PCR was applied to validate and profile the expression of the novel miRNAs in 10 tissues. Some novel miRNAs, such as ipu-miR-129b, ipu-miR-7562 and ipu-miR-7553, were expressed in all tissues examined. However, some novel miRNAs appear to be tissue specific. Ipu-miR-7575 is predominantly expressed in stomach. Ipu-miR-7147 and ipu-miR-203c are highly expressed in heart, but are relatively weakly expressed in other tissues. Based on sequence complementarity between miRNAs and mRNA targets, potential target sequences for the 45 novel miRNAs were identified by searching for antisense hits in the reference RNA sequences of the channel catfish. These potential target sequences are involved in immune regulation, transcriptional regulation, metabolism and many other biological functions. The discovery of miRNAs in the channel catfish genome by this study contributes to a better understanding of the role miRNAs play in regulating diverse biological processes in fish and vertebrates.

The innate immune-related genes in catfish

Catfish is one of the most important aquaculture species in America (as well as in Asia and Africa). In recent years, the production of catfish has suffered massive financial losses due to pathogen spread and breakouts. Innate immunity plays a crucial role in increasing resistance to pathogenic organisms and has generated increasing interest in the past few years. This review summarizes the current understanding of innate immune-related genes in catfish, including pattern recognition receptors, antimicrobial peptides, complements, lectins, cytokines, transferrin and gene expression profiling using microarrays and next generation sequencing technologies. This review will benefit the understanding of innate immune system in catfish and further efforts in studying the innate immune-related genes in fish.

Bioinformatic identification and validation of conservative microRNAs in Ictalurus punctatus

Catfish (Ictalurus spp.) is an important aquaculture species around the world, accounting for over 60 % of the domestic aquaculture output in the United States. However, little information is available about I. punctatus miRNAs which play an important role in the regulation of almost every biological process. In the present studies, we applied a bioinformatic strategy to identify 16 miRNAs which represent 12 miRNA families in I. punctatus by searching both expressed sequence tags and genome survey sequences databases. The A + U contents of the candidate pre-miRNA sequence range from 51 to 63 %, and the pre-miRNA sequences vary from 55 to 63 bp in length. To verify the predicted miRNAs, real-time PCR was used to profile the expression of 16 miRNAs with different tissues of I. punctatus. All the miRNA candidates were detectable in five tissues except for ipu-miR-9-3p. Based on sequence complementarity between miRNAs and their mRNA targets, potential targets for I. punctatus miRNAs were predicted. Due to the limited information for the I. punctatus transcripts, only one sequence targeted by ipu-miR-135 was identified to be an I. punctatus EB1 mRNA. Bioinformatic analyses indicated that the 3' untranslated region (3'-UTR) of EB1 mRNA contains an ipu-miR-135 target site, which are perfectly complementary to the seed region (positions 2-8) of the mature ipu-miR-135. I. punctatus miRNAs characterized in this study may provide useful information for the miRNAs research in I. punctatus and other aquaculture species.

Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map

Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ∼52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds.

Pathogen recognition receptors in channel catfish: II. Identification, phylogeny and expression of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs)

Vertebrates including teleost fish have evolved an array of pathogen recognition receptors (PRRs) for detecting and responding to various pathogen-associated molecular patterns (PAMPs), including Toll-like receptors (TLRs), nucleotide-binding domain, leucine-rich repeat containing receptors (NLRs), and the retinoic acid inducible gene I (RIG-I) like receptors (RLRs). As a part of the series of studies targeted to characterize catfish PRRs, we described 22 NLR receptors in the sister contribution. Here in this study, we focused on cytosolic PRRs recognizing nucleotide pathogen-associated molecular patterns (PAMPs) of invading viruses, the retinoic acid-inducible gene I (RIG-I)-like receptors (RLR receptors). Three RLRs with DExD/H domain containing RNA helicases, retinoic acid inducible gene-I (RIG-I), melanoma differentiation-associated gene 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2), were identified from channel catfish, Ictalurus punctatus. The catfish RIG-I encodes 937 amino acids that contains two CARDs, a DExDc, a HELICc and a RD domains. MDA5 encodes 1005 amino acids with all the domains identified for RIG-I. LGP2 encodes 677 amino acids that contain other domains but not the CARD domain at the N-terminus. Phylogenetic analyses of the three genes of catfish showed close clustering with their counterparts from other teleost fish. All the genes were found to be constitutively expressed in various tissues of catfish with minor variations. Channel catfish ovarian cells when infected with channel catfish virus showed significant increase in the transcript abundance of all the three genes. Further, RLR genes showed significant increases in expression in the liver tissue collected at different time-points after bacterial infection as well. The results indicate that the catfish RLRs may play important roles in antiviral and anti-bacterial immune responses.

Identification and comparative analysis of the Eriocheir sinensis microRNA transcriptome response to Spiroplasma eriocheiris infection using a deep sequencing approach

The Chinese mitten crab Eriocheir sinensis is one of the most important freshwater aquaculture crustacean species in China. MicroRNAs (miRNAs) are small non-coding RNAs that are important effectors in the intricate host-pathogen interaction network. To increase the repertoire of miRNAs characterized in crustaceans and to examine the relationship between host miRNA expression and pathogen infection, we used the Illumina/Solexa deep sequencing technology to sequence two small RNA libraries prepared from haemocytes of E. sinensis under normal conditions and during infection with Spiroplasma eriocheiris. The high-throughput sequencing resulted in approximately 30,975,151 and 30,826,277 raw reads corresponding to 12,077,088 and 16,271,545 high-quality mappable reads for the normal and infected haemocyte samples, respectively. Bioinformatic analyses identified 735 unique miRNAs, including 36 that are conserved in crustaceans, 134 that are novel to crabs but are present in other arthropods (PN-type), and 565 that are completely new (PC-type). Two hundred twenty-eight unique miRNAs displayed significant differential expression between the normal and infected haemocyte samples (p < 0.0001). Of these, 133 (58%) were significantly up-regulated and 95 (42%) were significantly down-regulated upon challenge with S. eriocheiris. Real-time quantitative PCR (RT-qPCR) experiments were preformed for 10 miRNAs of the two samples, and agreement was found between the sequencing and RT-qPCR data. To our knowledge, this is the first report of comprehensive identification of E. sinensis miRNAs and of expression analysis of E. sinensis miRNAs after exposure to S. eriocheiris. Many miRNAs were differentially regulated when exposed to the pathogen, and these findings support the hypothesis that certain miRNAs might be essential in host-pathogen interactions. Our results suggest that elucidation of the molecular mechanisms responsible for miRNA regulation of the host's innate immune system should help with the development of new control strategies to prevent or treat S. eriocheiris infections in crustaceans.

Alternative complement pathway of channel catfish (Ictalurus punctatus): molecular characterization, mapping and expression analysis of factors Bf/C2 and Df

The complement system is important in both innate and adaptive host defense against microbial infection in vertebrates. It contains three pathways: the classical, alternative, and lectin pathways. Complement component factors B and D are two crucial proteases in the alternative pathway. In this study, the genes of complement factors Bf/C2 and Df from channel catfish, Ictalurus punctatus were identified and characterized. Two complement factor B-related genes, Bf/C2A and Bf/C2B, and factor D gene Df were identified. Phylogenetic analysis suggested that Bf/C2A and Bf/C2B is likely orthologous to factor B and factor C2, respectively. Southern blot results suggested that these three genes are all single-copy genes in the catfish genome. The catfish Bf/C2A, Bf/C2B and Df genes were genetically mapped on linkage group 3, 20 and 29, respectively. Bf/C2A and Bf/C2B are highly expressed in liver and kidney, while Df is highly expressed in gill and spleen. After infection with Edwardsiella ictaluri, the expression of Bf/C2A, Bf/C2B and Df genes were found to be remarkably induced in the gill, liver, spleen and kidney at some sampling times, indicating that these three complement factors play a pivotal role in immune responses after the bacterial infection in catfish.

Biotechnologies for the management of genetic resources for food and agriculture

In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.

A pilot study for channel catfish whole genome sequencing and de novo assembly

Background

Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for de novo sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs.

Results

A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp.

Conclusions

A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.