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1.
Int J Genomics ; 2020: 5940205, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32904540

RESUMO

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

2.
G3 (Bethesda) ; 10(10): 3497-3504, 2020 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-32747341

RESUMO

Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 90% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or an average of one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics.

3.
Proc Natl Acad Sci U S A ; 117(26): 15305-15315, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32541052

RESUMO

Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa, RdDM is required in the maternal sporophyte for successful seed development. Here, we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during B. rapa seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in diverse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together, these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.


Assuntos
Brassica rapa/embriologia , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Regulação da Expressão Gênica de Plantas/fisiologia , RNA de Plantas , Sementes/crescimento & desenvolvimento , Alelos , Arabidopsis/metabolismo , Brassica rapa/genética , Brassica rapa/crescimento & desenvolvimento , Brassica rapa/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Interferente Pequeno , Sementes/genética , Sementes/metabolismo
4.
Clin Exp Allergy ; 50(7): 848-868, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32306538

RESUMO

BACKGROUND: Brassica rapeseed crops contain high concentrations of oil in the seed. The remaining meal, following oil extraction, has a high protein content, but is of low value due to the presence of high amounts of napin seed storage proteins. These 2S albumin-like proteins are difficult to digest and have been identified as major allergens in humans. OBJECTIVE: To comprehensively characterize the napin gene (NG) family in Brassica rapa and to gain an understanding of the structural basis of allergenicity of the expressed proteins. METHODS: To identify candidate napin genes in B rapa, 2S albumin-like napin genes of Arabidopsis thaliana were used as query sequences to search for similarity against the B rapa var. pekinensis Chiifu-401 v2 and the var. trilocularis R-o-18 v1.5 genomes. Multiple sequence alignment (MSA) and epitope modelling was carried out to determine structural and evolutionary relationships of NGs and their potential allergenicity. RESULTS: Four candidate napin genes in R-o-18 and ten in Chiifu-401 were identified with high sequence similarity to A thaliana napin genes. Multiple sequence alignment revealed strong conservation among the candidate genes. An epitope survey indicated high conservation of allergenic epitope motifs with known 2S albumin-like allergens. CONCLUSION: Napin is thought to be responsible for a  high prevalence of food allergies. Characterization of the napin gene family in B rapa will give important insight into the protein structure, and epitope modelling will help to advance studies into allergenicity including the development of precise diagnostic screenings and therapies for this potential food allergy as well as the possible manipulation of napin levels in the seed by gene editing technology.

5.
Matern Child Health J ; 24(6): 748-758, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32285334

RESUMO

OBJECTIVE: Floods are one of the most common types of disasters in Bangladesh and lead to direct and indirect impacts on health. The aim of the study was to assess the impact of floods on Maternal and Newborn Healthcare (MNH) utilization in Bangladesh between the years 2011 and 2014. METHODS: We used variables from the Bangladesh Demographic and Health Survey 2014 data and georeferenced data of floods between 2011 and 2014 from the Emergency Events Database. Multivariate logistic regression was used to determine whether the flood-affected exposures were significant in predicting differences in MNH utilization. RESULTS: The odds for the received antenatal care by skilled providers, institutional deliveries, deliveries by c-section, and postnatal care of the babies were significantly lower (Unadjusted OR = 0.81, 0.88, 0.83, and 0.82 respectively; P < 0.05) in the flood-affected area than the non-affected area. Additionally, the odds of postnatal checkup of women was statistically significant (P < 0.001) and less likely to be received in flood-affected area (OR = 0.76). The odds of all indicators were significantly lower (OR < 1) for the women living in the twice and four times flooded areas compared to the once flooded areas. CONCLUSIONS FOR PRACTICE: The study shows that floods can have a negative impact on MNH utilization. In addition, repeated floods have a worse impact on MNH utilization than incidental floods. Extra effort should be put on ensuring access to MNH of women in flood-affected areas.

6.
Sci Rep ; 10(1): 5048, 2020 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-32193408

RESUMO

The Proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.

7.
BMC Genomics ; 21(1): 199, 2020 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-32131725

RESUMO

BACKGROUND: Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. Traits investigated were: nut weight (NW), kernel weight (KW), kernel recovery (KR), percentage of whole kernels (WK), tree trunk circumference (TC), percentage of racemes that survived from flowering through to nut set, and number of nuts per raceme. RESULTS: Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of < 0.05), and four with WK. Multiple regression, as well as mapping of markers to genome assembly scaffolds suggested that some SNPs were detecting the same QTL. There were 44 significant SNPs identified for TC although multiple regression suggested detection of 16 separate QTLs. CONCLUSIONS: These findings have important implications for macadamia breeding, and highlight the difficulties of heterozygous populations with rapid LD decay. By coupling validated marker-trait associations detected through GWAS with MAS, genetic gain could be increased by reducing the selection time for economically important nut characteristics. Genomic selection may be a more appropriate method to predict complex traits like tree size and yield.


Assuntos
Macadamia/crescimento & desenvolvimento , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Biologia Computacional , Estudo de Associação Genômica Ampla , Técnicas de Genotipagem , Macadamia/genética , Fenótipo , Melhoramento Vegetal , Proteínas de Plantas/genética
8.
PLoS One ; 14(8): e0221578, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31442274

RESUMO

Rapeseed oil (canola, Brassica napus L.) is an important healthy vegetable oil throughout the world, the nutritional and economical value of which largely depends on its seed fatty acid composition. In this study, based on 201,187 SNP markers developed from the SLAF-seq (specific locus amplified fragment sequencing), a genome wide association study of four important fatty acid content traits (erucic acid, oleic acid, linoleic acid and linolenic acid) in a panel of 300 inbred lines of rapeseed in two environments (JXAU and JXRIS) was carried out. A total of 148 SNP loci significantly associated with these traits were detected by MLM model analysis respectively, and 30 SNP loci on A08 and C03 chromosomes were detected in three traits of erucic acid, oleic acid and linoleic acid contents simultaneously. Furthermore, 108 highly favorable alleles for increasing oleic acid and linoleic acid content, also for decreasing erucic acid content simultaneously were observed. By a basic local alignment search tool (BLAST) search with in a distance of 100 Kb around these significantly SNP-trait associations, we identified 20 orthologs of the functional candidate genes related to fatty acid biosynthesis, including the known vital fatty acid biosynthesis genes of BnaA.FAE1 and BnaC. FAE1 on the A08 and C03 chromosomes, and other potential candidate genes involving in the fatty acid biosynthesis pathway, such as the orthologs genes of FAD2, LACS09, KCS17, CER4, TT16 and ACBP5. This study lays a basis for uncovering the genetic variations and the improvement of fatty acid composition in B. napus.


Assuntos
Brassica napus/genética , Ácidos Graxos/metabolismo , Genes de Plantas , Loci Gênicos , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único/genética , Ecótipo , Regulação da Expressão Gênica de Plantas , Fenótipo , Característica Quantitativa Herdável
9.
Genome Biol Evol ; 11(7): 1965-1970, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-31263885

RESUMO

Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda.


Assuntos
Anti-Helmínticos/farmacologia , Genoma Helmíntico/genética , Haemonchus/efeitos dos fármacos , Haemonchus/genética , Animais , Sequência de Bases , Genômica , Nova Zelândia
10.
BMC Res Notes ; 12(1): 362, 2019 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-31248431

RESUMO

OBJECTIVES: Black Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest. DATA DESCRIPTION: The genomic DNA of a local (Chattogram, Bangladesh) healthy male Black Bengal goat (Capra hircus) was extracted and then sequenced. Sequencing was completed using the Illumina HiSeq 2500 sequencing platform and the draft assembly was generated using the "ARS1" genome as the reference. MAKER gene annotation pipeline was utilized to annotate 26,458 gene models. Genome completeness was assessed using BUSCO (Benchmarking Universal Single-Copy Orthologs) which showed 82.5% completeness of the assembled genome.


Assuntos
Genoma , Cabras/genética , Animais , Masculino , Anotação de Sequência Molecular , Análise de Sequência de DNA
11.
BMC Res Notes ; 11(1): 921, 2018 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-30577879

RESUMO

OBJECTIVE: Hilsa shad (Tenualosa ilisha), is a popular fish of Bangladesh belonging to the Clupeidae family. An anadromous species, like the salmon and many other migratory fish, it is a unique species that lives in the sea and travels to freshwater rivers for spawning. During its entire life, Tenualosa ilisha migrates both from sea to freshwater and vice versa. DATA DESCRIPTION: The genome of Tenualosa ilisha collected from the river Padma of Rajshahi, Bangladesh has been sequenced and its de novo hybrid assembly and structural annotations are being reported here. Illumina and PacBio sequencing platforms were used for high depth sequencing and the draft genome assembly was found to be 816 MB with N50 size of 188 kb. MAKER gene annotation tool predicted 31,254 gene models. Benchmarking Universal Single-Copy Orthologs refer 95% completeness of the assembled genome.


Assuntos
Peixes/genética , Genoma/genética , Animais , Bangladesh , Água Doce , Água do Mar
12.
PLoS One ; 13(9): e0203654, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30212503

RESUMO

Plant phosphorus (P) remobilisation during leaf senescence has fundamental implications for global P cycle fluxes. Hypothesising that genes involved in remobilisation of P from leaves during grain filling would show altered expression in response to P deprivation, we investigated gene expression in rice flag leaves at 8 days after anthesis (DAA) and 16 DAA in plants that received a continuous supply of P in the nutrient solution vs plants where P was omitted from the nutrient solution for 8 consecutive days prior to measurement. The transcriptional response to growth in the absence of P differed between the early stage (8 DAA) and the later stage (16 DAA) of grain filling. At 8 DAA, rice plants maintained production of energy substrates through upregulation of genes involved in photosynthesis. In contrast, at 16 DAA carbon substrates were produced by degradation of structural polysaccharides and over 50% of highly upregulated genes in P-deprived plants were associated with protein degradation and nitrogen/amino acid transport, suggesting withdrawal of P from the nutrient solution led to accelerated senescence. Genes involved in liberating inorganic P from the organic P compounds and vacuolar P transporters displayed differential expression depending on the stage of grain filling stage and timing of P withdrawal.


Assuntos
Grão Comestível/metabolismo , Oryza/metabolismo , Fósforo/metabolismo , Carbono/metabolismo , Metabolismo Energético/genética , Regulação da Expressão Gênica de Plantas , Nitrogênio/metabolismo , Oryza/genética , Oryza/crescimento & desenvolvimento , Fotossíntese/genética , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA de Plantas/química , RNA de Plantas/metabolismo
13.
Heredity (Edinb) ; 121(1): 87-104, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29523839

RESUMO

Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles. Many Myrtaceae are grown commercially for terpene products including the eucalypts Corymbia and Eucalyptus. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is largely conserved in the closely related E. globulus. However, the TPS gene family has been well studied only in these two eucalypt species. The recent assembly of two Corymbia citriodora subsp. variegata genomes presents an opportunity to examine the conservation of this important gene family across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp. variegata revealed a similar overall number, and relative subfamily representation, to that previously reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied considerably between Eucalyptus and Corymbia, with several instances of translocation, expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in primary metabolism than those involved in secondary metabolism, likely reflecting different selective constraints. The variation in cluster size within subfamilies and the broad conservation between the eucalypts in the face of this variation are discussed, highlighting the potential contribution of selection, concerted evolution and stochastic processes. These findings provide the foundation to better understand terpene evolution within the ecologically and economically important Myrtaceae.


Assuntos
Alquil e Aril Transferases/genética , Biologia Computacional , Evolução Molecular , Variação Genética , Família Multigênica , Myrtaceae/genética , Mapeamento Cromossômico , Biologia Computacional/métodos , Dosagem de Genes , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Genômica/métodos , Anotação de Sequência Molecular , Myrtaceae/classificação , Myrtaceae/enzimologia , Filogenia , Locos de Características Quantitativas
14.
Plant J ; 94(4): 575-582, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29569777

RESUMO

Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction. Here we show that, unlike Arabidopsis, mutations in the Pol IV-dependent small RNA pathway cause severe and specific reproductive defects in Brassica rapa. High rates of abortion occur when seeds have RdDM mutant mothers, but not when they have mutant fathers. Although abortion occurs after fertilization, RdDM function is required in maternal somatic tissue, not in the female gametophyte or the developing zygote, suggesting that siRNAs from the maternal soma might function in filial tissues. We propose that recently outbreeding species such as B. rapa are key to understanding the role of RdDM during plant reproduction.


Assuntos
Brassica rapa/genética , Metilação de DNA , RNA Interferente Pequeno/genética , Sementes/genética , Brassica rapa/embriologia , Brassica rapa/enzimologia , Brassica rapa/fisiologia , Elementos de DNA Transponíveis/genética , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Diploide , Genótipo , Mutação , Fenótipo , Melhoramento Vegetal , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA de Plantas/genética , Reprodução , Sementes/embriologia , Sementes/enzimologia , Sementes/fisiologia
15.
Plant Biotechnol J ; 15(1): 15-26, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27228336

RESUMO

The physiology and molecular regulation of phosphorus (P) remobilization from vegetative tissues to grains during grain filling is poorly understood, despite the pivotal role it plays in the global P cycle. To test the hypothesis that a subset of genes involved in the P starvation response are involved in remobilization of P from flag leaves to developing grains, we conducted an RNA-seq analysis of rice flag leaves during the preremobilization phase (6 DAA) and when the leaves were acting as a P source (15 DAA). Several genes that respond to phosphate starvation, including three purple acid phosphatases (OsPAP3, OsPAP9b and OsPAP10a), were significantly up-regulated at 15 DAA, consistent with a role in remobilization of P from flag leaves during grain filling. A number of genes that have not been implicated in the phosphate starvation response, OsPAP26, SPX-MFS1 (a putative P transporter) and SPX-MFS2, also showed expression profiles consistent with involvement in P remobilization from senescing flag leaves. Metabolic pathway analysis using the KEGG system suggested plastid membrane lipid synthesis is a critical process during the P remobilization phase. In particular, the up-regulation of OsPLDz2 and OsSQD2 at 15 DAA suggested phospholipids were being degraded and replaced by other lipids to enable continued cellular function while liberating P for export to developing grains. Three genes associated with RNA degradation that have not previously been implicated in the P starvation response also showed expression profiles consistent with a role in P mobilization from senescing flag leaves.


Assuntos
Grão Comestível/genética , Regulação da Expressão Gênica de Plantas , Oryza/genética , Oryza/metabolismo , Fósforo/metabolismo , Folhas de Planta/metabolismo , Análise de Sequência de RNA/métodos , Envelhecimento , Sequência de Bases , Mapeamento Cromossômico , Genes de Plantas/genética , Metabolismo dos Lipídeos , Redes e Vias Metabólicas/genética , Fósforo/análise , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Regulação para Cima
16.
BMC Genomics ; 17(1): 937, 2016 11 17.
Artigo em Inglês | MEDLINE | ID: mdl-27855648

RESUMO

BACKGROUND: The large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes. Despite a long history of research, comparative analyses in the Proteaceae and macadamia breeding programs are restricted by a paucity of genetic information. To address this, we sequenced the genome and transcriptome of the widely grown Macadamia integrifolia cultivar 741. RESULTS: Over 95 gigabases of DNA and RNA-seq sequence data were de novo assembled and annotated. The draft assembly has a total length of 518 Mb and spans approximately 79% of the estimated genome size. Following annotation, 35,337 protein-coding genes were predicted of which over 90% were expressed in at least one of the leaf, shoot or flower tissues examined. Gene family comparisons with five other eudicot species revealed 13,689 clusters containing macadamia genes and 1005 macadamia-specific clusters, and provides evidence for linage-specific expansion of gene families involved in pathogen recognition, plant defense and monoterpene synthesis. Cyanogenesis is an important defense strategy in the Proteaceae, and a detailed analysis of macadamia gene homologues potentially involved in cyanogenic glycoside biosynthesis revealed several highly expressed candidate genes. CONCLUSIONS: The gene space of macadamia provides a foundation for comparative genomics, gene discovery and the acceleration of molecular-assisted breeding. This study presents the first available genomic resources for the large basal eudicot family Proteaceae, access to most macadamia genes and opportunities to uncover the genetic basis of traits of importance for adaptation and crop improvement.


Assuntos
Genoma de Planta , Genômica , Macadamia/genética , Transcriptoma , Biologia Computacional/métodos , Ontologia Genética , Genômica/métodos , Glicosídeos/biossíntese , Sequenciamento de Nucleotídeos em Larga Escala , Macadamia/metabolismo , Anotação de Sequência Molecular , Família Multigênica
17.
Mar Drugs ; 14(7)2016 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-27447649

RESUMO

Dicathais orbita is a mollusc of the Muricidae family and is well known for the production of the expensive dye Tyrian purple and its brominated precursors that have anticancer properties, in addition to choline esters with muscle-relaxing properties. However, the biosynthetic pathways that produce these secondary metabolites in D. orbita are not known. Illumina HiSeq 2000 transcriptome sequencing of hypobranchial glands, prostate glands, albumen glands, capsule glands, and mantle and foot tissues of D. orbita generated over 201 million high quality reads that were de novo assembled into 219,437 contigs. Annotation with reference to the Nr, Swiss-Prot and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases identified candidate-coding regions in 76,152 of these contigs, with transcripts for many enzymes in various metabolic pathways associated with secondary metabolite biosynthesis represented. This study revealed that D. orbita expresses a number of genes associated with indole, sulfur and histidine metabolism pathways that are relevant to Tyrian purple precursor biosynthesis, and many of which were not found in the fully annotated genomes of three other molluscs in the KEGG database. However, there were no matches to known bromoperoxidase enzymes within the D. orbita transcripts. These transcriptome data provide a significant molecular resource for gastropod research in general and Tyrian purple producing Muricidae in particular.


Assuntos
Vias Biossintéticas/genética , Colina/metabolismo , Ésteres/metabolismo , Gastrópodes/genética , Indóis/metabolismo , Moluscos/genética , Transcriptoma/genética , Animais , Austrália , Bases de Dados Genéticas , Gastrópodes/metabolismo , Anotação de Sequência Molecular/métodos , Moluscos/metabolismo , Peroxidases/metabolismo
18.
PLoS One ; 10(10): e0140725, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26488885

RESUMO

Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita.


Assuntos
Gastrópodes/microbiologia , Indóis/metabolismo , Microbiota/genética , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Animais , Técnicas de Tipagem Bacteriana , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Sequência de Bases , Biodiversidade , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Proteobactérias/genética , Proteobactérias/isolamento & purificação , Análise de Sequência de DNA , Spirochaetales/genética , Spirochaetales/isolamento & purificação , Tenericutes/genética , Tenericutes/isolamento & purificação
19.
BMC Genomics ; 15 Suppl 9: S13, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25522147

RESUMO

BACKGROUND: Sequence data from the chloroplast genome have played a central role in elucidating the evolutionary history of flowering plants, Angiospermae. In the past decade, the number of complete chloroplast genomes has burgeoned, leading to well-supported angiosperm phylogenies. However, some relationships, particulary among early-diverging lineages, remain unresolved. The diverse Southern Hemisphere plant family Proteaceae arose on the ancient supercontinent Gondwana early in angiosperm history and is a model group for adaptive radiation in response to changing climatic conditions. Genomic resources for the family are limited, and until now it is one of the few early-diverging 'basal eudicot' lineages not represented in chloroplast phylogenomic analyses. RESULTS: The chloroplast genome of the Australian nut crop tree Macadamia integrifolia was assembled de novo from Illumina paired-end sequence reads. Three contigs, corresponding to a collapsed inverted repeat, a large and a small single copy region were identified, and used for genome reconstruction. The complete genome is 159,714 bp in length and was assembled at deep coverage (3.29 million reads; ~2000 x). Phylogenetic analyses based on 83-gene and inverted repeat region alignments, the largest sequence-rich datasets to include the basal eudicot family Proteaceae, provide strong support for a Proteales clade that includes Macadamia, Platanus and Nelumbo. Genome structure and content followed the ancestral angiosperm pattern and were highly conserved in the Proteales, whilst size differences were largely explained by the relative contraction of the single copy regions and expansion of the inverted repeats in Macadamia. CONCLUSIONS: The Macadamia chloroplast genome presented here is the first in the Proteaceae, and confirms the placement of this family with the morphologically divergent Plantanaceae (plane tree family) and Nelumbonaceae (sacred lotus family) in the basal eudicot order Proteales. It provides a high-quality reference genome for future evolutionary studies and will be of benefit for taxon-rich phylogenomic analyses aimed at resolving relationships among early-diverging angiosperms, and more broadly across the plant tree of life.


Assuntos
Genoma de Cloroplastos/genética , Macadamia/genética , DNA de Plantas/genética , Evolução Molecular , Genômica , Sequências Repetidas Invertidas/genética , Repetições de Microssatélites/genética , Filogenia , Análise de Sequência de DNA
20.
Database (Oxford) ; 2014: bau020, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24647628

RESUMO

The laboratory mouse is the most widely used mammalian model organism in biomedical research, so a thorough annotation of functional variation in the mouse genome would be of significant value. In this study, we compared sequence variation in a comprehensive list of functional elements (e.g. promoters, enhancers and CTCF binding sites) across 17 inbred mouse strains. Sequences were derived for ∼300,000 functional elements experimentally identified by the mouse ENCODE project as regulating gene expression in 19 different tissue sources. We aligned sequences for each predicted cis-regulatory element to genomes of 17 mouse strains. This yielded a database comprising ∼5 million aligned sequences, allowing interrogation of sequence variation of functional elements for each of the 19 tissues/cell types in commonly used mouse strains. We also developed an online tool to visualize the genome around each predicted cis-regulatory element in each tissue context and which allows efficient comparison of variation between any two sets of strains. This will be particularly useful in the context of the Collaborative Cross (CC), which was conceived as a powerful new systems genetics resource to accelerate gene discovery. Comprising a large number of inbred strains derived from eight genetically diverse founders, the CC offers rapid mapping and identification of genes that mediate complex traits. We show that, among the 17 sequenced strains, the set of CC founder strains captures the most variability in the ENCODE elements, further emphasizing the value of this resource. Database URL: www.sysgen.org/ecco.


Assuntos
Variação Genética , Genoma/genética , Sequências Reguladoras de Ácido Nucleico/genética , Transcriptoma/genética , Animais , Sequência de Bases , Bases de Dados Genéticas , Efeito Fundador , Camundongos , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Reprodutibilidade dos Testes
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