Identification and characterization of insect-specific proteins by genome data analysis

Molecular Characterization of Odorant-Binding Protein Genes Associated with Host-Seeking Behavior in Oides leucomelaena

The identification of odorant-binding proteins (OBPs) involved in host location by Oides leucomelaena (O. leucomelaena Weise, 1922, Coleoptera, Galerucinae) is significant for its biological control. Tools in the NCBI database were used to compare and analyze the transcriptome sequences of O. leucomelaena with OBP and other chemosensory-related proteins of other Coleoptera insects. Subsequently, MEGA7 was utilized for OBP sequence alignment and the construction of a phylogenetic tree, combined with expression profiling to screen for candidate antennae-specific OBPs. In addition, fumigation experiments with star anise volatiles were conducted to assess the antennae specificity of the candidate OBPs. Finally, molecular docking was employed to speculate on the binding potential of antennae-specific OBPs with star anise volatiles. The study identified 42 candidate OBPs, 8 chemosensory proteins and 27 receptors. OleuOBP3, OleuOBP5, and OleuOBP6 were identified as classic OBP family members specific to the antennae, which was confirmed by volatile fumigation experiments. Molecular docking ultimately clarified that OleuOBP3, OleuOBP5, and OleuOBP6 all exhibit a high affinity for β-caryophyllene among the star anise volatiles. We successfully obtained three antennae-specific OBPs from O. leucomelaena and determined their high-affinity volatiles, providing a theoretical basis for the development of attractants in subsequent stages.

TLR pathway signaling molecules in burbot (Lota lota): molecular characterization, basal expression, and their response to Poly(I:C)

Burbot (Lota lota), a fish species of economic and ecological significance found across northern hemisphere freshwater ecosystems, was the focus of this study. We characterized 19 Toll-like receptor (TLR) genes in burbot, tracing their expression patterns following pathogen exposure. TLR genes, crucial to the innate immune system, including TLR13-1/2/3, TLR2/2-2/2-3/2-4/2-5, and TLR22a/22b/22c/22d, were discovered to be tandemly repeated, signifying an evolution in the fish's immune system. Notably, different TLR subfamilies displayed tissue-specific expressions, with TLR1 primarily in spleen and head kidney, TLR13 in head kidney, trunk kidney, and heart, TLR22 in trunk kidney and liver, and TLR3 and TLR9 predominantly in spleen and head kidney, but also in trunk kidney. Further, we investigated the response of TLR genes in burbot to pathogen exposure using qRT-PCR. This involved measuring mRNA expressions of identified TLR genes in spleen and liver tissues after injecting Poly(I:C) to simulate a double-stranded RNA viral infection. The results revealed a time and tissue-specific expression pattern. Specifically, LoTLR3 reached peak expression in the spleen 12 h post-injection, declining thereafter, while TLR2 subfamily members only began expressing after 24 h. In the liver, activation of the TLR3-IRF7 and TLR3-IRF3 signaling pathways was noted. Integrating these results with transcriptomic data illuminated the pivotal role of TLR genes in the burbot's immune response. Such findings are vital in shaping future disease prevention and treatment strategies.

Expression and purification of snustorr snarlik protein from Plutella xylostella

Snustorr snarlik (Snsl) is a type of extracellular protein essential for insect cuticle formation and insect survival, but is absent in mammals, making it a potential selective target for pest control. Here, we successfully expressed and purified the Snsl protein of Plutella xylostella in Escherichia coli. Two truncated forms of Snsl protein, Snsl 16-119 and Snsl 16-159, were expressed as a maltose-binding protein (MBP) fusion protein and purified to a purity above 90% after a five-step purification protocol. Snsl 16-119, forming stable monomer in solution, was crystallized, and the crystal was diffracted to a resolution of ∼10 Å. Snsl 16-159, forming an equilibrium between monomer and octamer in solution, was shown to form rod-shaped particles on negative staining electron-microscopy images. Our results lay a foundation for the determination of the structure of Snsl, which would improve our understanding of the molecular mechanism of cuticle formation and related pesticide resistance and provide a template for structure-based insecticide design.

The genome of a mangrove plant, Avicennia marina, provides insights into adaptation to coastal intertidal habitats

Whole-genome duplication, gene family and lineage-specific genes analysis based on high-quality genome reveal the adaptation mechanisms of Avicennia marina to coastal intertidal habitats. Mangrove plants grow in a complex habitat of coastal intertidal zones with high salinity, hypoxia, etc. Therefore, it is an interesting question how mangroves adapt to the unique intertidal environment. Here, we present a chromosome-level genome of the Avicennia marina, a typical true mangrove with a size of 480.43 Mb, contig N50 of 11.33 Mb and 30,956 annotated protein-coding genes. We identified 621 Avicennia-specific genes that are mainly related to flavonoid and lignin biosynthesis, auxin homeostasis and response to abiotic stimulus. We found that A. marina underwent a novel specific whole-genome duplication, which is in line with a brief era of global warming that occurred during the paleocene-eocene maximum. Comparative genomic and transcriptomic analyses outline the distinct evolution and sophisticated regulations of A. marina adaptation to the intertidal environments, including expansion of photosynthesis and oxidative phosphorylation gene families, unique genes and pathways for antibacterial, detoxifying antioxidant and reactive oxygen species scavenging. In addition, we also analyzed salt gland secretion-related genes, and those involved in the red bark-related flavonoid biosynthesis, while significant expansions of key genes such as NHX, 4CL, CHS and CHI. High-quality genomes in future investigations will facilitate the understand of evolution of mangrove and improve breeding.

Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes

Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.

Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea Plant Camellia sinensis

Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

Lineage-specific gene evolution of innate immunity in Bombyx mori to adapt to challenge by pathogens, especially entomopathogenic fungi

Bombyx mori is a model species of Lepidoptera, in which 21 gene families and 220 genes have been identified as involved in immunity. However, only 45 B. mori - Drosophila melanogaster - Anopheles gambiae - Apis mellifera - Tribolium castaneum 1:1:1:1:1 orthologous genes were identified. B. mori has unique immune factors not found in D. melanogaster - A. gambiae - A. mellifera - T. castaneum. Pattern recognition receptors, signal transducers and effector genes for antifungal immune responses in B. mori have evolved through expansion and modification of existing genes. This review summarizes the current knowledge of the antifungal immune responses of B. mori and focuses on the lineage-specific gene evolution used by Lepidoptera to adapt to the challenge by pathogens, especially entomopathogenic fungi.

Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum

Lineage-specific genes (LSGs) are the genes that have no recognizable homology to any sequences in other species, which are important drivers for the generation of new functions, phenotypic changes, and facilitating species adaptation to environment. Aegiceras corniculatum is one of major mangrove plant species adapted to waterlogging and saline conditions, and the exploration of aegiceras-specific genes (ASGs) is important to reveal its adaptation to the harsh environment. Here, we performed a systematic analysis on ASGs, focusing on their sequence characterization, origination and expression patterns. Our results reveal that there are 4823 ASGs in the genome, approximately 11.84% of all protein-coding genes. High proportion (45.78%) of ASGs originate from gene duplication, and the time of gene duplication of ASGs is consistent with the timing of two genome-wide replication (WGD) events that occurred in A. corniculatum, and also coincides with a short period of global warming during the Paleocene-Eocene Maximum (PETM, 55.5 million years ago). Gene structure analysis showed that ASGs have shorter protein lengths, fewer exons, and higher isoelectric point. Expression patterns analysis showed that ASGs had low levels of expression and more tissue-specific expression. Weighted gene co-expression network analysis (WGCNA) revealed that 86 ASGs co-expressed gene modules were primarily involved in pathways related to adversity stress, including plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, peroxisome and pentose phosphate pathway. This study provides a comprehensive analysis of the characteristics and potential functions of ASGs and identifies key candidate genes, which will contribute to the subsequent further investigation of the adaptation of A. corniculatum to intertidal coastal wetland habitats.

Genome-wide identification, characterization and expression analysis of lineage-specific genes within Hanseniaspora yeasts

Lineage-specific genes (LSGs) are defined as genes with sequences that are not significantly similar to those in any other lineage. LSGs have been proposed, and sometimes shown, to have significant effects in the evolution of biological function. In this study, two sets of Hanseniaspora spp. LSGs were identified by comparing the sequences of the Kloeckera apiculata genome and of 80 other yeast genomes. This study identified 344 Hanseniaspora-specific genes (HSGs) and 109 genes ('orphan genes') specific to K. apiculata. Three thousand three hundred thirty-one K. apiculata genes that showed significant similarity to at least one sequence outside the Hanseniaspora were classified into evolutionarily conserved genes. We analyzed their sequence features, functional categories, gene origin, gene structure and gene expression. We also investigated the predicted cellular roles and Gene Ontology categories of the LSGs using functional inference. The patterns of the functions of LSGs do not deviate significantly from genome-wide average. The results showed that a few LSGs were formed by gene duplication, followed by rapid sequence divergence. Many of the HSGs and orphan genes exhibited altered expression in response to abiotic stress. Studying these LSGs might be helpful for understanding the molecular mechanism of yeast adaption.

Mapping Selection within Drosophila melanogaster Embryo's Anatomy

We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns, and development with the aim of mapping adaptation over the entire embryo's anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-based annotations of in situ hybridization data directly from the BDGP database, Tomancak et al. 2007) and the polymorphism and divergence in these genes (from the project DGRP, Mackay et al. 2012).The proportion of nonsynonymous substitutions that are adaptive, neutral, or slightly deleterious are estimated for the set of genes expressed in each embryonic anatomical structure using the distribution of fitness effects-alpha method (Eyre-Walker and Keightley 2009). This method is a robust derivative of the McDonald and Kreitman test (McDonald and Kreitman 1991). We also explore whether different anatomical structures differ in the phylogenetic age, codon usage, or expression bias of the genes they express and whether genes expressed in many anatomical structures show more adaptive substitutions than other genes.We found that: 1) most of the digestive system and ectoderm-derived structures are under selective constraint, 2) the germ line and some specific mesoderm-derived structures show high rates of adaptive substitution, and 3) the genes that are expressed in a small number of anatomical structures show higher expression bias, lower phylogenetic ages, and less constraint.

A database for orphan genes in Poaceae

Orphan genes refer to a group of protein-coding genes lacking recognizable homologs in the other organisms. Extensive studies have demonstrated that numerous newly sequenced genomes contain a significant number of orphan genes, which have important roles in plant's responses to the environment. Due to a lack of phylogenetic conservation, the origin of orphan genes and their functions are currently not well defined. In the present study, a Poaceae orphan genes database (POGD; http://bioinfo.ahau.edu.cn/pogd) was established to serve as a user-friendly web interface for entry browsing, searching and downloading orphan genes from various plants. Four Poaceae species, including Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, are included in the current version of POGD. The database provides gene descriptions (chromosome strands, physical location), gene product records (protein length, isoelectric point, molecular weight as well as gene and protein sequences) and functional annotations (cellular role, gene ontology category, subcellular localization prediction). Basic Local Alignment Search Tool and comparative analyses were also provided on the website. POGD will serve as a comprehensive and reliable repository, which will help uncover regulatory mechanisms of orphan genes and may assist in the development of comparative genomics in plant biology.

Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?

Background

Current genome sequencing projects reveal substantial numbers of taxonomically restricted, so called orphan genes that lack homology with genes from other evolutionary lineages. However, it is not clear to what extent orphan genes are real, genomic artifacts, or represent non-coding RNAs.

Results

Here, we use a simple set of assumptions to test the nature of orphan genes. First, a sequence that is transcribed is considered a real biological entity. Second, every sequence that is supported by proteome data or shows a depletion of non-synonymous substitutions is a protein-coding gene. Using genomic, transcriptomic and proteomic data for the nematode Pristionchus pacificus, we show that between 4129–7997 (42–81 %) of predicted orphan genes are expressed and 3818–7545 (39–76 %) of orphan genes are under negative selection. In three cases that exhibited strong evolutionary constraint but lacked expression evidence in 14 RNA-seq samples, we could experimentally validate the predicted gene structures. Comparing different data sets to infer selection on orphan gene clusters, we find that the presence of a closely related genome provides the most powerful resource to robustly identify evidence of negative selection. However, even in the absence of other genomic data, the availability of paralogous sequences was enough to show negative selection in 8–10 % of orphan genes.

Conclusions

Our study shows that the great majority of previously identified orphan genes in P. pacificus are indeed protein-coding genes. Even though this work represents a case study on a single species, our approach can be transferred to genomic data of other non-model organisms in order to ascertain the protein-coding nature of orphan genes.

Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis)

Background

With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions.

Results

Two set of citrus LSGs, 296 citrus-specific genes (CSGs) and 1039 orphan genes specific to sweet orange, were identified by comparative analysis between the sweet orange genome sequences and 41 genomes and 273 transcriptomes. With the two sets of genes, gene structure and gene expression pattern were investigated. On average, both the CSGs and orphan genes have fewer exons, shorter gene length and higher GC content when compared with those evolutionarily conserved genes (ECs). Expression profiling indicated that most of the LSGs expressed in various tissues of sweet orange and some of them exhibited distinct temporal and spatial expression patterns. Particularly, the orphan genes were preferentially expressed in callus, which is an important pluripotent tissue of citrus. Besides, part of the CSGs and orphan genes expressed responsive to abiotic stress, indicating their potential functions during interaction with environment.

Conclusion

This study identified and characterized two sets of LSGs in citrus, dissected their sequence features and expression patterns, and provided valuable clues for future functional analysis of the LSGs in sweet orange.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2211-z) contains supplementary material, which is available to authorized users.

Data in support of genome-wide identification of lineage-specific genes within Caenorhabditis elegans

Two sets of LSGs were identified using BLAST: Caenorhabditis elegans species-specific genes (SSGs, 1423), and Caenorhabditis genus-specific genes (GSGs, 4539). The data contained in this article show SSGs and GSGs have significant differences in evolution and that most of them were formed by gene duplication and integration of transposable elements (TEs). Subsequent observation of temporal expression and protein function presents that many SSGs and GSGs are expressed and that genes involved with sex determination, specific stress, immune response, and morphogenesis are most represented. The data are related to research article "Genome-wide identification of lineage-specific genes within Caenorhabditis elegans" in Journal of Genomics [1].

Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

With the rapid growth of sequencing technology, a number of genomes and transcriptomes of various species have been sequenced, contributing to the study of lineage-specific genes (LSGs). We identified two sets of LSGs using BLAST: one included Caenorhabditis elegans species-specific genes (1423, SSGs), and the other consisted of Caenorhabditis genus-specific genes (4539, GSGs). The subsequent characterization and analysis of the SSGs and GSGs showed that they have significant differences in evolution and that most LSGs were generated by gene duplication and integration of transposable elements (TEs). We then performed temporal expression profiling and protein function prediction and observed that many SSGs and GSGs are expressed and that genes involved with sex determination, specific stress, immune response, and morphogenesis are over-represented, suggesting that these specific genes may be related to the Caenorhabditis nematodes' special ability to survive in severe and extreme environments.

Fruit flies in biomedical research

Many scientists complain that the current funding situation is dire. Indeed, there has been an overall decline in support in funding for research from the National Institutes of Health and the National Science Foundation. Within the Drosophila field, some of us question how long this funding crunch will last as it demotivates principal investigators and perhaps more importantly affects the long-term career choice of many young scientists. Yet numerous very interesting biological processes and avenues remain to be investigated in Drosophila, and probing questions can be answered fast and efficiently in flies to reveal new biological phenomena. Moreover, Drosophila is an excellent model organism for studies that have translational impact for genetic disease and for other medical implications such as vector-borne illnesses. We would like to promote a better collaboration between Drosophila geneticists/biologists and human geneticists/bioinformaticians/clinicians, as it would benefit both fields and significantly impact the research on human diseases.

Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees

Whether coding or regulatory sequence change is more important to the evolution of phenotypic novelty is one of biology's major unresolved questions. The field of evo-devo has shown that in early development changes to regulatory regions are the dominant mode of genetic change, but whether this extends to the evolution of novel phenotypes in the adult organism is unclear. Here, we conduct ten RNA-Seq experiments across both novel and conserved tissues in the honey bee to determine to what extent postdevelopmental novelty is based on changes to the coding regions of genes. We make several discoveries. First, we show that with respect to novel physiological functions in the adult animal, positively selected tissue-specific genes of high expression underlie novelty by conferring specialized cellular functions. Such genes are often, but not always taxonomically restricted genes (TRGs). We further show that positively selected genes, whether TRGs or conserved genes, are the least connected genes within gene expression networks. Overall, this work suggests that the evo-devo paradigm is limited, and that the evolution of novelty, postdevelopment, follows additional rules. Specifically, evo-devo stresses that high network connectedness (repeated use of the same gene in many contexts) constrains coding sequence change as it would lead to negative pleiotropic effects. Here, we show that in the adult animal, the converse is true: Genes with low network connectedness (TRGs and tissue-specific conserved genes) underlie novel phenotypes by rapidly changing coding sequence to perform new-specialized functions.

Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish

BACKGROUND

The genomic basis of teleost phenotypic complexity remains obscure, despite increasing availability of genome and transcriptome sequence data. Fish-specific genome duplication cannot provide sufficient explanation for the morphological complexity of teleosts, considering the relatively large number of extinct basal ray-finned fishes.

RESULTS

In this study, we performed comparative genomic analysis to discover the Conserved Teleost-Specific Genes (CTSGs) and orphan genes within zebrafish and found that these two sets of lineage-specific genes may have played important roles during zebrafish embryogenesis. Lineage-specific genes within zebrafish share many of the characteristics of their counterparts in other species: shorter length, fewer exon numbers, higher GC content, and fewer of them have transcript support. Chromosomal location analysis indicated that neither the CTSGs nor the orphan genes were distributed evenly in the chromosomes of zebrafish. The significant enrichment of immunity proteins in CTSGs annotated by gene ontology (GO) or predicted ab initio may imply that defense against pathogens may be an important reason for the diversification of teleosts. The evolutionary origin of the lineage-specific genes was determined and a very high percentage of lineage-specific genes were generated via gene duplications. The temporal and spatial expression profile of lineage-specific genes obtained by expressed sequence tags (EST) and RNA-seq data revealed two novel properties: in addition to being highly tissue-preferred expression, lineage-specific genes are also highly temporally restricted, namely they are expressed in narrower time windows than evolutionarily conserved genes and are specifically enriched in later-stage embryos and early larval stages.

CONCLUSIONS

Our study provides the first systematic identification of two different sets of lineage-specific genes within zebrafish and provides valuable information leading towards a better understanding of the molecular mechanisms of the genomic basis of teleost phenotypic complexity for future studies.

Identification of microRNAs in Helicoverpa armigera and Spodoptera litura based on deep sequencing and homology analysis

The current identification of microRNAs (miRNAs) in insects is largely dependent on genome sequences. However, the lack of available genome sequences inhibits the identification of miRNAs in various insect species. In this study, we used a miRNA database of the silkworm Bombyx mori as a reference to identify miRNAs in Helicoverpa armigera and Spodoptera litura using deep sequencing and homology analysis. Because all three species belong to the Lepidoptera, the experiment produced reliable results. Our study identified 97 and 91 conserved miRNAs in H. armigera and S. litura, respectively. Using the genome of B. mori and BAC sequences of H. armigera as references, 1 novel miRNA and 8 novel miRNA candidates were identified in H. armigera, and 4 novel miRNA candidates were identified in S. litura. An evolutionary analysis revealed that most of the identified miRNAs were insect-specific, and more than 20 miRNAs were Lepidoptera-specific. The investigation of the expression patterns of miR-2a, miR-34, miR-2796-3p and miR-11 revealed their potential roles in insect development. miRNA target prediction revealed that conserved miRNA target sites exist in various genes in the 3 species. Conserved miRNA target sites for the Hsp90 gene among the 3 species were validated in the mammalian 293T cell line using a dual-luciferase reporter assay. Our study provides a new approach with which to identify miRNAs in insects lacking genome information and contributes to the functional analysis of insect miRNAs.

How microbiology helps define the rhizome of life

In contrast to the tree of life (TOF) theory, species are mosaics of gene sequences with different origins. Observations of the extensive lateral sequence transfers in all organisms have demonstrated that the genomes of all life forms are collections of genes with different evolutionary histories that cannot be represented by a single TOF. Moreover, genes themselves commonly have several origins due to recombination. The human genome is not free from recombination events, so it is a mosaic like other organisms' genomes. Recent studies have demonstrated evidence for the integration of parasitic DNA into the human genome. Lateral transfer events have been accepted as major contributors of genome evolution in free-living bacteria. Furthermore, the accumulation of genomic sequence data provides evidence for extended genetic exchanges in intracellular bacteria and suggests that such events constitute an agent that promotes and maintains all bacterial species. Archaea and viruses also form chimeras containing primarily bacterial but also eukaryotic sequences. In addition to lateral transfers, orphan genes are indicative of the fact that gene creation is a permanent and unsettled phenomenon. Currently, a rhizome may more adequately represent the multiplicity and de novo creation of a genome. We wanted to confirm that the term “rhizome” in evolutionary biology applies to the entire cellular life history. This view of evolution should resemble a clump of roots representing the multiple origins of the repertoires of the genes of each species.

The influence of rickettsiologists on post-modern microbiology

Many of the definitions in microbiology are currently false. We have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the lifestyle of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins), and in many cases, gene loss is significantly inked to the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for mammal infection. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function, and interactions of the major microbial communities, but it neglects the minority populations. Finally, Darwin’s descent with modification theory, as represented by the tree of life, no longer matches our current genomic knowledge because genomics has revealed the occurrence of de novo-created genes and the mosaic structure of genomes, the Rhizome of life is therefore more appropriate.

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee

Background

Studies have shown that taxonomically restricted genes are significant in number and important for the evolution of lineage specific traits. Social insects have gained many novel morphological and behavioral traits relative to their solitary ancestors. The task repertoire of an advanced social insect, for example, can be 40-50 tasks, about twice that of a solitary wasp or bee. The genetic basis of this expansion in behavioral repertoire is still poorly understood, and a role for taxonomically restricted genes has not been explored at the whole genome level.

Results

Here we present comparative genomics results suggesting that taxonomically restricted genes may have played an important role in generating the expansion of behavioral repertoire associated with the evolution of eusociality. First, we show that the current honey bee official gene set contains about 700 taxonomically restricted genes. These are split between orphans, genes found only in the Hymenoptera, and genes found only in insects. Few of the orphans or genes restricted to the Hymenoptera have been the focus of experimental work, but several of those that have are associated with novel eusocial traits or traits thought to have changed radically as a consequence of eusociality. Second, we predicted that if taxonomically restricted genes are important for generating novel eusocial traits, then they should be expressed with greater frequency in workers relative to the queen, as the workers exhibit most of the novel behavior of the honey bee relative to their solitary ancestors. We found support for this prediction. Twice as many taxonomically restricted genes were found amongst the genes with higher expression in workers compared to those with higher expression in queens. Finally, we compiled an extensive list of candidate taxonomically restricted genes involved in eusocial evolution by analyzing several caste specific gene expression data sets.

Conclusions

This work identifies a large number of candidate taxonomically restricted genes that may have played a role in eusocial evolution. This work thus lays the foundation for future functional genomics work on the evolution of novelty in the context of social behavior. We also present preliminary evidence, based on biased patterns of gene expression, that taxonomically restricted genes may have played a role in the evolution of caste systems, a characteristic lineage specific social trait.

Chitin research revisited

Two centuries after the discovery of chitin, it is widely accepted that this biopolymer is an important biomaterial in many aspects. Numerous studies on chitin have focused on its biomedical applications. In this review, various aspects of chitin research including sources, structure, biosynthesis, chitinolytic enzyme, chitin binding protein, genetic engineering approach to produce chitin, chitin and evolution, and a wide range of applications in bio- and nanotechnology will be dealt with.

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species

Background

With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs) is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics. Genes with no apparent orthologs between the bovine and human genome may be responsible for major differences between the species, however, such genes are often neglected in functional genomics studies.

Results

A BLAST-based method was exploited to explore the current annotation and orthology predictions in Ensembl. Genes with no orthologs between the two genomes were classified into groups based on alignments, ontology, manual curation and publicly available information. Starting from a high quality and specific set of orthology predictions, as provided by Ensembl, hidden relationship between genes and genomes of different mammalian species were unveiled using a highly sensitive approach, based on sequence similarity and genomic comparison.

Conclusions

The analysis identified 3,801 bovine genes with no orthologs in human and 1010 human genes with no orthologs in cow, among which 411 and 43 genes, respectively, had no match at all in the other species. Most of the apparently non-orthologous genes may potentially have orthologs which were missed in the annotation process, despite having a high percentage of identity, because of differences in gene length and structure. The comparative analysis reported here identified gene variants, new genes and species-specific features and gave an overview of the other side of orthology which may help to improve the annotation of the bovine genome and the knowledge of structural differences between species.

Evolution of primate orphan proteins

Genomes contain a large number of genes that do not have recognizable homologues in other species. These genes, found in only one or a few closely related species, are known as orphan genes. Their limited distribution implies that many of them are probably involved in lineage-specific adaptive processes. One important question that has remained elusive to date is how orphan genes originate. It has been proposed that they might have arisen by gene duplication followed by a period of very rapid sequence divergence, which would have erased any traces of similarity to other evolutionarily related genes. However, this explanation does not seem plausible for genes lacking homologues in very closely related species. In the present article, we review recent efforts to identify the mechanisms of formation of primate orphan genes. These studies reveal an unexpected important role of transposable elements in the formation of novel protein-coding genes in the genomes of primates.

Generation, annotation, and analysis of ESTs from midgut tissue of adult female Anopheles stephensi mosquitoes

Background

Malaria is a tropical disease caused by protozoan parasite, Plasmodium, which is transmitted to humans by various species of female anopheline mosquitoes. Anopheles stephensi is one such major malaria vector in urban parts of the Indian subcontinent. Unlike Anopheles gambiae, an African malaria vector, transcriptome of A. stephensi midgut tissue is less explored. We have therefore carried out generation, annotation, and analysis of expressed sequence tags from sugar-fed and Plasmodium yoelii infected blood-fed (post 24 h) adult female A. stephensi midgut tissue.

Results

We obtained 7061 and 8306 ESTs from the sugar-fed and P. yoelii infected mosquito midgut tissue libraries, respectively. ESTs from the combined dataset formed 1319 contigs and 2627 singlets, totaling to 3946 unique transcripts. Putative functions were assigned to 1615 (40.9%) transcripts using BLASTX against UniProtKB database. Amongst unannotated transcripts, we identified 1513 putative novel transcripts and 818 potential untranslated regions (UTRs). Statistical comparison of annotated and unannotated ESTs from the two libraries identified 119 differentially regulated genes. Out of 3946 unique transcripts, only 1387 transcripts were mapped on the A. gambiae genome. These also included 189 novel transcripts, which were mapped to the unannotated regions of the genome. The EST data is available as ESTDB at .

Conclusion

3946 unique transcripts were successfully identified from the adult female A. stephensi midgut tissue. These data can be used for microarray development for better understanding of vector-parasite relationship and to study differences or similarities with other malaria vectors. Mapping of putative novel transcripts from A. stephensi on the A. gambiae genome proved fruitful in identification and annotation of several genes. Failure of some novel transcripts to map on the A. gambiae genome indicates existence of substantial genomic dissimilarities between these two potent malaria vectors.

Conservation of domain structure in a fast-evolving heterochromatic SUUR protein in drosophilids

Different genomic regions replicate at a distinct time during S-phase. The SuUR mutation alters replication timing and the polytenization level of intercalary and pericentric heterochromatin in Drosophila melanogaster salivary gland polytene chromosomes. We analyzed SuUR in different insects, identified conserved regions in the protein, substituted conserved amino acid residues, and studied effects of the mutations on SUUR function. SuUR orthologs were identified in all sequenced drosophilids, and a highly divergent ortholog was found in the mosquito genome. We demonstrated that SUUR evolves at very high rate comparable with that of Transformer. Remarkably, upstream ORF within 5' UTR of the gene is more conserved than SUUR in drosophilids, but it is absent in the mosquito. The domain structure and charge of SUUR are maintained in drosophilids despite the high divergence of the proteins. The N-terminal part of SUUR with similarity to the SNF2/SWI2 proteins displays the highest level of conservation. Mutation of two conserved amino acid residues in this region impairs binding of SUUR to polytene chromosomes and reduces the ability of the protein to cause DNA underreplication. The least conserved middle part of SUUR interacting with HP1 retains positively and negatively charged clusters and nuclear localization signals. The C terminus contains interlacing conserved and variable motifs. Our results suggest that SUUR domains evolve with different rates and patterns but maintain their features.

Insect-Specific microRNA Involved in the Development of the Silkworm Bombyx mori

MicroRNAs (miRNAs) are endogenous non-coding genes that participate in post-transcription regulation by either degrading mRNA or blocking its translation. It is considered to be very important in regulating insect development and metamorphosis. We conducted a large-scale screening for miRNA genes in the silkworm Bombyx mori using sequence-by-synthesis (SBS) deep sequencing of mixed RNAs from egg, larval, pupal, and adult stages. Of 2,227,930 SBS tags, 1,144,485 ranged from 17 to 25 nt, corresponding to 256,604 unique tags. Among these non-redundant tags, 95,184 were matched to the silkworm genome. We identified 3,750 miRNA candidate genes using a computational pipeline combining RNAfold and TripletSVM algorithms. We confirmed 354 miRNA genes using miRNA microarrays and then performed expression profile analysis on these miRNAs for all developmental stages. While 106 miRNAs were expressed in all stages, 248 miRNAs were egg- and pupa-specific, suggesting that insect miRNAs play a significant role in embryogenesis and metamorphosis. We selected eight miRNAs for quantitative RT-PCR analysis; six of these were consistent with our microarray results. In addition, we searched for orthologous miRNA genes in mammals, a nematode, and other insects and found that most silkworm miRNAs are conserved in insects, whereas only a small number of silkworm miRNAs has orthologs in mammals and the nematode. These results suggest that there are many miRNAs unique to insects.

Origin of primate orphan genes: a comparative genomics approach

Genomes contain a large number of genes that do not have recognizable homologues in other species and that are likely to be involved in important species-specific adaptive processes. The origin of many such "orphan" genes remains unknown. Here we present the first systematic study of the characteristics and mechanisms of formation of primate-specific orphan genes. We determine that codon usage values for most orphan genes fall within the bulk of the codon usage distribution of bona fide human proteins, supporting their current protein-coding annotation. We also show that primate orphan genes display distinctive features in relation to genes of wider phylogenetic distribution: higher tissue specificity, more rapid evolution, and shorter peptide size. We estimate that around 24% are highly divergent members of mammalian protein families. Interestingly, around 53% of the orphan genes contain sequences derived from transposable elements (TEs) and are mostly located in primate-specific genomic regions. This indicates frequent recruitment of TEs as part of novel genes. Finally, we also obtain evidence that a small fraction of primate orphan genes, around 5.5%, might have originated de novo from mammalian noncoding genomic regions.