Molecular Evolution of Rice Blast Resistance Gene bsr-d1

Rice blast,caused by the fungus Magnaporthe oryzae,reduces rice yields by 10%to 35%.Incorporating blast resistance genes into breeding programs is an effective strategy to combat this disease.Understanding the genetic variants that confer resistance is crucial to this strategy.The gene Bsr-d1 encodes a C2H2-like transcription factor,and its recessive allele confers broad-spectrum resistance against infections by various strains of M.oryzae.In this study,we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice accessions.Our results revealed that wild rice exhibited significantly higher nucleotide diversity,with polymorphic regions primarily concentrated in the promoter region,in contrast to indica and japonica rice varieties.The Bsr-d1 gene displayed significant differentiation between indica and japonica rice varieties,with the bsr-d1 resistance allele being unique to indica rice.Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula.Moreover,we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene.In summary,our study uncovering the origin and evolution of bsr-d1 will enhance our understanding of resistance gene variation and expedite the resistance breeding process.

Recent Progress in Elucidating the Structure, Function and Evolution of Disease Resistance Genes in Plants

Plants employ multifaceted mechanisms to fight with numerous pathogens in nature. Resistance （R） genes are the most effective weapons against pathogen invasion since they can specifically recognize the corresponding pathogen effectors or associated protein（s） to activate plant immune responses at the site of infection. Up to date, over 70 R genes have been isolated from various plant species. Most R proteins contain conserved motifs such as nucleotide-binding site （NBS）, leucine-rich repeat （LRR）, Toll-interleukin-1 receptor domain （TIR, homologous to cytoplasmic domains of the Drosophila Toll protein and the manamalian intefleukin-1 receptor）, coiled-coil （CC） or leucine zipper （LZ） structure and protein kinase domain （PK）. Recent results indicate that these domains play significant roles in R protein interactions with effector proteins from pathogens and in activating signal transduction pathways involved in innate immunity. This review highlights an overview of the recent progress in elucidating the structure, function and evolution of the isolated R genes in different plant-pathogen interaction systems.

Sequence Variation and Molecular Evolution of Hormone-Sensitive Lipase Genes in Species of Bovidae

The partial sequences of exon Ⅰ of hormone-sensitive lipase （HSL） genes in yak （Bos grunniens）, cattle （Bos taurus）, zebu （Bos indicus）, and buffalo （Bubalus bubalis） were analyzed. Comparisons of these sequences and the deduced amino acid sequences with the homologous HSL gene and protein sequences in other mammalian species including pig （Sus scrofa）, human （Homo sapiens）, mouse （Mus musculus）, and rat （Rattus sp.） retrieved from the GenBank were carried out and finally a phylogenetic tree was constructed using the partial DNA sequences of the HSL genes in all species. The results showed that the homologies of the partial exon Ⅰ sequences of the HSL genes between yak and cattle, zebu, buffalo, pig, human, mouse, and rat were as high as 99.8%, 99.6%, 97.4%, 90.6%, 88.4%, 83.5%, and 82.3%, respectively. This was accompanied by highly homologous amino acid sequences of the HSLs： 100%, 100%, 98.2%, 94.0%, 92.2%, 89.8%, and 89.8% identity, respectively. There are more transitions, less transversions, and no insertion or deletion in variable nucleotides of the HSL genes between the yak and other species. The majority of the variable mutations was synonymous and was found most frequently at the third codon, followed by the first and second codons, a finding that was in accordance with the neutralism hypothesis for molecular evolution. In the phylogenetic tree, the cattle and zebu were clustered together first, followed by the yak, buffalo, pig, human, mouse, and rat. This was in agreement with taxonomy suggesting that the partial sequences of exon Ⅰ of the HSL genes were useful in constructing the phylogenetic tree of mammalian species. Among the four species of Bovidae, genetic differentiation in the HSL genes between yak and buffalo is equivalent to that between buffalo and cattle and between buffalo and zebu. Furthermore, the genetic distances in the HSL genes are much smaller between yak, cattle, and zebu than those between each of the three species and the buffalo. Therefore, it is reasonable to consider yak as an independent species of the genus Bos.

Diversity of Bmp15 and Gdf9 Genes in White Goat of Guizhou Province and Evolution of the Encoded Proteins

Members of the transforming growth factor-beta superfamily, growth differentiation factor 9 （GDF9） and bone morphogenetic protein 15 （BMP 15）, have crucial roles in fecundity of sheep. Our previous investigation confirmed that the fecundity mutations of sheep presented in highly prolific White goat individuals of Guizhou province. To illuminate other polymorphisms in Bmpl5 and Gdfl） genes and the relationship of these mutations with function, we cloned and characterized the coding region of Bmp15 and Gdfl）. Molecular models of BMP15 and GDF9 mature peptide of White goat were constructed based on the homology of human BMP7 experimental tertiary structure. Two exons encoded prepropeptide of 394 amino acids in BMPI5 and 453 residues in GDF9, respectively. Apart from the FecXs mutation （S99I） in BMP15 and V791 mutation in GDF9 confirmed in White goat previously, other seven and three polymorphism sites were detected from BMP15 and GDF9 mature peptides, respectively. S32G, N66H, S99I/P99I and G107R in BMP15 could be important for the binding of dimer to receptors. Changes of P78Q and V79I in GDF9 might affect the binding of dimer to receptor type t. Comparing the length of BMP 15 and GDF9 prepropeptide in vertebrates, an increase in length of BMP 15 presented along with the protein evolution from fish to mammal and the divergence of the N-terminus residues in matured BMP15 peptide might contribute to the sensitive control on the fertility of animal species with low ovulation rate. These findings gave a valuable explanation for the correlation of mutations in Bmpl5 and Gdfl） genes with the control on fecundity of White goat and supported the notion that they were the pivotal factors in female fertility of White goat in Guizhou province.

Molecular Composition and Evolution of the Chalcone Synthase (CHS) Gene Family in Five Species of Camellia (Theaceae)

The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from total DNA by PCR method. Three sequences of the fifth species in Camellia and two sequences of Glycine max as the designated outgroups were obtained from GenBank. Our results indicated that CHS gene family in Camellia was differentiated to three subfamilies (A, B, C) during the evolutionary history with six groups (A1, A2, A3, BI, B2, C). Among them, only group A2 was possessed by all five species in this study. However, the other five groups were detected only in some species of the plants studied. All members of CHS gene family in this study had high sequence similarity, more than 90% among the members in the same subfamily and more than 78% among different subfamilies at nucleotide level., According to the estimated components of amino acids, the function of CHS genes in Camellia had been diverged. The nucleotide substitutions of the different groups were not identical. Based on phylogenetic analyse inferred from sequences of CHS genes and their deduced amino acid sequences, we concluded that the CHS genes with new function in this genus were evolved either by mutations on several important sites or by accumulation of the mutations after the gene duplication. A further analysis showed that the diversification of CHS genes in Camellia still occurred recently, and the evolutionary models were different to some extant among different species. So we assumed that the different evolutionary models resulted from the impacts of variable environmental elements after the events of speciation.

Phenylalanine ammonia-lyase gene families in cucurbit species: Structure, evolution, and expression

Phenylalanine ammonia-lyase （PAL）, the first enzyme of phenylpropanoid pathway, is always encoded by multigene families in plants. In this study, using genome-wide searches, 13 PAL genes in cucumber （CsPAL1-13） and 13 PALs in melon （Cm- PALl-13） were identified. In the corresponding genomes, ten of these PAL genes were located in tandem in two clusters, while the others were widely dispersed in different chromosomes as a single copy. The protein sequences of CsPALs and CmPALs shared an overall high identity to each other. In our previous report, 12 PAL genes were identified in watermelon （CIPAL1-12）. Thereby, a total of 38 cucurbit PAL members were included. Here, a comprehensive comparison of PAL gene families was performed among three cucurbit plants. The phylogenetic and syntenic analyses placed the cucurbit PALs as 11 CsPAL-CmPAL-CIPAL triples, of which ten triples were clustered into the dicot group, and the remaining one, CsPAL1-CmPAL8-CIPAL2, was grouped with gymnosperm PALs and might serve as an ancestor of cucurbit PALs. By comparing the syntenic relationships and gene structure of these PAL genes, the expansion of cucurbit PAL families might arise from a series of segmental and tandem duplications and intron insertion events. Furthermore, the expression profiling in different tissues suggested that different cucurbit PALs displayed divergent but overlapping expression profiles, and the CsPAL-CmPAL-CIPAL orthologs showed correlative expression patterns among three cucurbit plants. Taken together, this study provided an extensive description on the evolution and expression of cucurbit PAL gene families and might facilitate the further studies for elucidating the functions of PALs in cucurbit plants.

Molecular evolution of the rice miR395 gene family

MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.

Study on Origin and Evolution of Polyploids in Parakmeria Hu et Cheng Using LEAFY Gene

[Objective] This study aimed to explore the origin and evolution of poly- poids in Parakmeria Hu et Cheng through LEAFY gene clone and sequence analysis. [Method] In this study, LEAFY gene in Parakmeria species and its relative genera was cloned and sequenced using molecular biology methods. With reference to LEAFY gene sequence published by NCBI, the origin pattern of polypoids in Parakmeria was explored and reasons for the distribution layout of different polypoids were analyzed through sequence alignment and phylogenetic analysis. [Result] Different Magnoliaceae species can be distinguished using the LEAFY gene, and there was a length polymorphism found in the 3＋ end of the LEAFY gene, which can be used to divide Magnoliaceae plants of different species or in different genera, thus of high application value. [Conclusion] Most Parakmeria tetraploids are produced by polyploidization of homologous chromosomes, while Parakmeria hexaploids are chiefly produced by both polyploidization of homologous chromosomes and heterologous hybridization.

Molecular characterization of LMW-GS genes from a somatic hybrid introgression line Ⅱ-12 between Triticum aestivum and Agropyron elongatum in relation to quick evolution

In order to exploit the evolution and find novel low-molecular-weight glutenin subunit （LMW-GS） for improvement of common wheat quality, thirteen variants from a somatic hybrid introgression line II-12 between Triticum aestivum cv. Jinan 177 （JN177） and Agropyron elongatum were characterized via genomic PCR. Four clones were pseudogenes because they contained an internal stop codon. The remaining nine variants contained intact open reading frames （ORFs）. Sequence alignment indicates that the proteins deduced from the nine ORFs have similar primary structure with LMW-GS cloned from its parents previously. However, they have some unique modifications in the structures. For example, EU292737 contains not only an extra Cys residue in the C-terminal domain but also a long repetitive domain. Both EU 159511 and EU292738 start their first Cys residue in the N-terminal repetitive domain, but not in the N-conserved domain traditionally. These structural alterations may have positive contributions to wheat flour quality. The results of phylogeny showed that most LMW-GS variances from 11-12 were homologous to those from parent JN177 and other wheat lines. The reason for quick evolution of LMW-GS in 11-12 was discussed.

Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

Mutants lacking wild-type MLO(Mildew resistance Locus O)proteins show broad-spectrum resistance to the powdery mildew fungus,and dysregulated cell death control,with spontaneous cell death in response to developmental or abiotic stimuli.In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants,we analysed systematically genome-wide data from Fragaria vesca,Prunus persica,Prunus mume,Malus domestica,Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods.Using three phylogenetic methods(the neighbour-joining,maximum likelihood,and Bayesian methods),we identified 117 MLO genes from 6 Rosaceae species.The results of all three phylogenetic analysis methods supported that these genes were divided into six clades.Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues.The findings indicated that motif 2 might be shared by the MLO gene family.The structural features of these genes showed large variations in sequence length among different species,although the lengths and the numbers of exons exhibited high degrees of similarity.Selective pressure analysis showed extremely significant differences in all 6 clades,with 2,1,and 1 site(s)under significant positive selection detected in clades III,IV,and VI,respectively.These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes.Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes.Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process.However,clade I may have undergone extensive altered functional constraints as a specialised functional role.Moreover,the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew,which then gradually evolved into functions such as the regulation of flower development,the control of root morphology,and seed evolution due to the different evolutionary rates after gene duplication.These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.

Genome-wide identification,evolutionary selection,and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea

DNA methylation plays an important role in plant growth and development,and in regulating the activity of transposable elements(TEs).Research on DNA methylation-related(DMR)genes has been reported in Arabidopsis,but little research on DMR genes has been reported in Brassica rapa and Brassica oleracea,the genomes of which exhibit significant differences in TE content.In this study,we identified 78 and 77 DMR genes in Brassica rapa and Brassica oleracea,respectively.Detailed analysis revealed that the numbers of DMR genes in different DMR pathways varied in B.rapa and B.oleracea.The evolutionary selection pressure of DMR genes in B.rapa and B.oleracea was compared,and the DMR genes showed differential evolution between these two species.The nucleotide diversity(π)and selective sweep(Tajima’s D)revealed footprints of selection in the B.rapa and B.oleracea populations.Transcriptome analysis showed that most DMR genes exhibited similar expression characteristics in B.rapa and B.oleracea.This study dissects the evolutionary differences and genetic variations of the DMR genes in B.rapa and B.oleracea,and will provide valuable resources for future research on the divergent evolution of DNA methylation between B.rapa and B.oleracea.

Evolution and phylogenetic application of the MC1R gene in the Cobitoidea(Teleostei: Cypriniformes)

Fish of the superfamily Cobitoidea sensu stricto （namely Ioaches） exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene （MCIR） plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MCIR gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae＋ （Cobitidae＋（Balitoridae＋Nemacheilidae））. Gene evolutionary analyses indicated that MCIR in Ioaches was under purifying selection pressure, with various sites having different dNIds values. Both Botiidae and Cobitidae had lower dN/ds values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoddae and Nemacheilidae, both had larger dNIds values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MCTR gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.

Rediscovery and analysis of Phytophthora carbohydrate esterase(CE) genes revealing their evolutionary diversity

A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.

The evolution of resistance gene in plants

Resistance genes enable plants to fight against plant pathogens. Plant resistance genes （R gene） are organized complexly in genome. Some resistance gene sequence data enable an insight into R gene structure and gene evolution. Some sites like Leucine-Rich Repeat （LRR） are of specific interest since homologous recombination can happen. Crossing over, transposon insertion and excision and mutation can produce new specificity. Three models explaining R gene evolution were discussed. More information needed for dissection of R gene evolution though some step can be inferred from genetic and sequence analysis.

Massive Molecular Parallel Evolution of the HSP90AA1 Gene between High-elevation Anurans

HSP90 AA1 is part of the heat shock protein 90 gene family and has important functions against heat stress. We report a case of molecular level parallel evolution of the HSP90 AA1 gene in high elevation amphibians. HSP90 AA1 gene sequences of four high-elevation anurans, Bufo gargarizans, Nanorana parkeri, Rana kukunoris, and Scutiger boulengeri, were compared along with five of their low-elevation relatives. A total of 16 amino-acid sites were identified as parallel evolution between N. parkeri and R. kukunoris. We generated both model based（Zhang and Kumar＇s test） and empirical data based（parallel/divergence plotting） null distributions for non-parallel evolution, and both methods clearly determined that the observed number of parallel substitutions were significantly more than the null expectation. Furthermore, on the HSP90 AA1 gene tree, N. parkeri and R. kukunoris formed a strongly supported clade that was away from their respective relatives. This study provides a clear case of molecular parallel evolution, which may have significant implications in understanding the genetic mechanisms of high-elevation adaptation.

Molecular Evolution of Visual Opsin Genes during the Behavioral Shifts between Different Photic Environments in Geckos

Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogeny and behavior on the structure of visual systems.In this study,we compared three opsin genes(RH2,LWS and SWS1)among 49 reptile species to detect positively selected genes as well as amino acid sites.Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1.Twelve positively selected sites were picked out for RH2 and LWS.Moreover,many diagnostic sites were found between geckos and non-gecko lizards,most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption(λ_(max)).The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.

Phylogenetic analysis of the five internal genes and evolutionary pathways of the Greek H3N8 equine influenza virus

To amplify the NS, NP, PB1, PB2 and PA internal genes of two equine H3N8 influenza A viruses isolated in Greece in 2003 and 2007 five primer pairs were designed. The derived sequences were analysed from a phylogenetic point of view and compared with the evolutionary patters of the HA and NA proteins. Comparison of nucleotide sequences of the five internal genes of the Greek strains showed high similarity (99.3% - 99.7%) to strains isolated from outbreaks in Europe and Asia during 2002-2008. A total of 11 amino acid substitutions of the surface protein NA and the RNP complex proteins were identified in the Greek strains compared to those of progenitor viruses circulating up to 2003. These substitutions were repeated in Chinese and Mongolian isolates from outbreaks in 2007-2008. Notably NS1 protein did not acquired amino acid substitutions and moreover, a stop codon introduced at position 220 was stably maintained in the Greek strains. Phylogenetic trees of the five internal genes did not show the same separation in clades. Greek strains classified them into the American sublineage (as for the PA) Florida clade II (as for the NP, NS1 and PB1) and among Chinese strains of 2007-2008 outbreaks (as for the PB2). Additionally, evolutionary profiles of these internal proteins, except PB2, indicated a parallel evolution fashion to the HA protein, suggesting the possible occurrence of genetic reassortment between H3N8 viruses of district evolutionary lineages. In conclusion, phylogenetic analysis of the internal genes reported in this study could establish a candidate framework for future scientific communications on the phylogenetic diversity and evolution of the equine influenza viruses.

Evolution of the ErbB gene family and analysis of regulators of Egfr expression during development of the rat spinal cord

Egfr,a member of the ErbB gene family,plays a critical role in tissue development and homeostasis,wound healing,and disease.However,expression and regulators of Egfr during spinal cord development remain poorly understood.In this study,we investigated ErbB evolution and analyzed co-expression modules,miRNAs,and transcription factors that may regulate Egfr expression in rats.We found that ErbB family members formed via Egfr duplication in the ancient ve rtebrates but dive rged after speciation of gnathostomes.We identified a module that was co-expressed with Egfr,which involved cell proliferation and blood vessel development.We predicted 25 miRNAs and nine transcription factors that may regulate Egfr expression.Dual-luciferase reporter assays showed six out of nine transcription factors significantly affected Egfr promoter reporter activity.Two of these transcription factors(KLF1 and STAT3)inhibited the Egfr promoter repo rter,whereas four transcription factors(including FOXA2)activated the Egfr promoter reporter.Real-time PCR and immunofluorescence expe riments showed high expression of FOXA2 during the embryonic period and FOXA2 was expressed in the floor plate of the spinal cord,suggesting the importance of FOXA2 during embryonic spinal cord development.Considering the importance of Egfr in embryonic spinal cord development,wound healing,and disease(specifically in cancer),regulatory elements identified in this study may provide candidate targets for nerve regeneration and disease treatment in the future.

Review. Comparative structures and evolution of mammalian lipase I (LIPI) genes and proteins: A close relative of vertebrate phospholipase LIPH

Lipase I (enzyme name LIPI or LPDL) (gene name LIPI [human] or Lipi [mouse]) is a phospholipase which generates 2-acyl lysophosphatidic acid (LPA), a lipid mediator required for maintaining homeostasis of diverse biological functions and in activating cell surface recaptors. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures and gene locations for LIPI genes and encoded proteins using data from several mammalian genome projects. LIPI is located on human chromosome 21 and is distinct from other phospholipase A1-like genes (LIPH and PS-PLA1). Mammalian LIPI genes contained 10 (human) or 11 (mouse) coding exons transcribed predominantly on the negative DNA strand. Mammalian LIPI protein subunits shared 61% - 99% sequence identities and exhibited sequence alignments and identities for key LIPI amino acid residues as well as extensive conservation of predicted secondary and tertiary structures with those previously reported for pancreatic lipase (PL), with “N-signal peptide”, “lipase” and “plat” structural domains. Comparative studies of mammalian LIPI sequences with LIPH, PS-PLA1 and pancreatic lipase (PL) confirmed predictions for LIPI N-terminal signal peptides (residues 1 - 15);predominantly conserved mammalian LIPI N-glycosylation sites (63NNSL and 396NISS for human LIPI);active site “triad” residues (Ser159;Asp183;His253);disulfide bond residues (238 - 251;275 - 286;289 - 297;436 - 455);and a 12 residue “active site lid”, which is shorter than for other lipases examined. Phylogenetic analyses supported a hypothesis that LIPI arose from a vertebrate LIPH gene duplication event within a mammalian common ancestral genome. In addition, LIPI, LIPH and PL-PLA1 genes were distinct from the vascular lipase (LIPG, LIPC and LPL) and pancreatic lipase (PL) gene families.

Fine-scale evolutionary genetic insights into Anopheles gambiae X-chromosome

Understanding the genetic architecture of indi-vidual taxa of medical importance is the first step for designing disease preventive strategies. To understand the genetic details and evolu-tionary perspective of the model malaria vector, Anopheles gambiae and to use the information in other species of local importance, we scanned the published X-chromosome se-quence for detail characterization and obtain evolutionary status of different genes. The te-locentric X-chromosome contains 106 genes of known functions and 982 novel genes. Majori-ties of both the known and novel genes are with introns. The known genes are strictly biased towards less number of introns;about half of the total known genes have only one or two in-trons. The extreme sized (either long or short) genes were found to be most prevalent (58% short and 23% large). Statistically significant positive correlations between gene length and intron length as well as with intron number and intron length were obtained signifying the role of introns in contributing to the overall size of the known genes of X-chromosome in An. gam-biae. We compared each individual gene of An. gambiae with 33 other taxa having whole ge-nome sequence information. In general, the mosquito Aedes aegypti was found to be ge-netically closest and the yeast Saccharomyces cerevisiae as most distant taxa to An. gambiae. Further, only about a quarter of the known genes of X-chromosome were unique to An. gambiae and majorities have orthologs in dif-ferent taxa. A phylogenetic tree was constructed based on a single gene found to be highly orthologous across all the 34 taxa. Evolutionary relationships among 13 different taxa were in-ferred which corroborate the previous and pre-sent findings on genetic relationships across various taxa.