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1.
PLoS One ; 9(1): e86728, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24497974

RESUMO

Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.


Assuntos
Arecaceae/genética , Metilação de DNA , Genes de Plantas , Resistência à Doença/genética , Etiquetas de Sequências Expressas , Ontologia Genética , MicroRNAs/genética , Repetições de Microssatélites , Anotação de Sequência Molecular , Filogenia , Folhas de Planta/genética , Proteínas de Plantas/genética , Polimorfismo de Nucleotídeo Único , RNA de Plantas/genética , Análise de Sequência de DNA , Fatores de Transcrição/genética , Transcriptoma
2.
Mol Cell Biochem ; 390(1-2): 9-18, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24378996

RESUMO

The growth and differentiation factor-11 (GDF-11) gene is thought to code for a single protein that plays a crucial role in regulating the development of multiple tissues. In this study, we aimed to investigate if the GDF-11 gene has another transcript and, if so, to characterise this transcript and determine its tissue-specific and developmental expression. We have identified a novel transcript of GDF-11 in mouse muscle, which contains the 3' region of intron 1, exon 2, exon 3 and 3'UTR, and has two transcription initiation sites and a single termination site. We named the novel transcript GDF-11ΔEx1 because it does not contain exon 1 of canonical GDF-11. The GDF-11ΔEx1 transcript was expressed in the skeletal muscles, heart, brain and kidney, but was undetectable in the liver and gut. The concentration of the GDF-11ΔEx1 transcript was increased in gastrocnemius muscles from three to 6 weeks of age, a period of accelerated muscle growth, steadily declined thereafter and was higher in male than female mice (P < 0.001 for age and sex). GDF-11ΔEx1 cDNA was predicted to code for a putative N-terminal-truncated propeptide and the canonical ligand for GDF-11. However, propeptide-specific antibodies could not identify proteins of the expected size in skeletal muscle. Interestingly, in silico analysis of the GDF-11ΔEx1 RNA predicted a secondary structure with the potential to coordinate multiple protein interactions as a molecular scaffold. Therefore, we postulate that GDF-11ΔEx1 may act as a long non-coding RNA to regulate the transcription of canonical GDF-11 and/or other genes in skeletal muscle and other tissues.


Assuntos
Proteínas Morfogenéticas Ósseas/biossíntese , Proteínas Morfogenéticas Ósseas/genética , Fatores de Diferenciação de Crescimento/biossíntese , Fatores de Diferenciação de Crescimento/genética , Isoformas de Proteínas/genética , RNA Longo não Codificante/genética , Sequência de Aminoácidos , Animais , Proteínas Morfogenéticas Ósseas/isolamento & purificação , Clonagem Molecular , DNA Complementar , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Fatores de Diferenciação de Crescimento/isolamento & purificação , Masculino , Camundongos , Dados de Sequência Molecular , Especificidade de Órgãos , Isoformas de Proteínas/isolamento & purificação , Homologia de Sequência
3.
J Mol Evol ; 74(5-6): 237-48, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22562705

RESUMO

The mammalian secreted ribonucleases (RNases) comprise a large family of structurally related proteins displaying considerable sequence variation, and have been used in evolutionary studies. RNase 1 (RNase A) has been assumed to play a role in digestion, while other members have been suggested to contribute to host defence. Using the recently assembled bovine genome sequence, we characterised the complete repertoire of genes present in the RNaseA family locus in cattle, and compared this with the equivalent locus in the human and mouse genomes. Several additions and corrections to the earlier analysis of the RNase locus in the mouse genome are presented. The bovine locus encodes 19 RNases, of which only six have unambiguous equivalent genes in the other two species. Chromosomal mapping and phylogenetic analysis indicate that a number of distinct gene duplication events have occurred in the cattle lineage since divergence from the human and mouse lineages. Substitution analysis suggests that some of these duplicated genes are under evolutionary pressure for purifying selection and may therefore be important to the physiology of cattle. Expression analysis revealed that individual RNases have a wide pattern of expression, including diverse mucosal epithelia and immune-related cells and tissues. These data clarify the full repertoire of bovine RNases and their relationships to those in humans and mice. They also suggest that RNase gene duplication within the bovine lineage accompanied by altered tissue-specific expression has contributed a survival advantage.


Assuntos
Bovinos/genética , Mapeamento Cromossômico , Regulação Enzimológica da Expressão Gênica , Loci Gênicos/genética , Filogenia , Ribonuclease Pancreático/genética , Ribonuclease Pancreático/metabolismo , Animais , DNA Complementar/genética , Etiquetas de Sequências Expressas , Duplicação Gênica/genética , Perfilação da Expressão Gênica , Genoma/genética , Humanos , Funções Verossimilhança , Camundongos , Homologia de Sequência de Aminoácidos
4.
Biochem Soc Trans ; 39(4): 1006-11, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21787338

RESUMO

Members of the protein family having similarity to BPI (bactericidal/permeability increasing protein) (the BPI-like proteins), also known as the PLUNC (palate, lung and nasal epithelium clone) family, have been found in a range of mammals; however, those in species other than human or mouse have been relatively little characterized. Analysis of the BPI-like proteins in cattle presents unique opportunities to investigate the function of these proteins, as well as address their evolution and contribution to the distinct physiology of ruminants. The present review summarizes the current understanding of the nature of the BPI-like locus in cattle, including the duplications giving rise to the multiple BSP30 (bovine salivary protein 30 kDa) genes from an ancestral gene in common with the single PSP (parotid secretory protein) gene found in monogastric species. Current knowledge of the expression of the BPI-like proteins in cattle is also presented, including their pattern of expression among tissues, which illustrate their independent regulation at sites of high pathogen exposure, and the abundance of the BSP30 proteins in saliva and salivary tissues. Finally, investigations of the function of the BSP30 proteins are presented, including their antimicrobial, lipopolysaccharide-binding and bacterial aggregation activities. These results are discussed in relation to hypotheses regarding the physiological role of the BPI-like proteins in cattle, including the role they may play in host defence and the unique aspects of digestion in ruminants.


Assuntos
Proteínas e Peptídeos Salivares/metabolismo , Animais , Bovinos , Expressão Gênica , Humanos , Saliva/metabolismo , Glândulas Salivares/metabolismo , Proteínas e Peptídeos Salivares/genética , Homologia Estrutural de Proteína
5.
Exp Dermatol ; 20(7): 582-8, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21554405

RESUMO

Keratin IF (KRT) and keratin-associated protein genes encode the majority of wool and hair proteins. We have identified cDNA sequences representing nine novel sheep KRT genes, increasing the known active genes from eight to 17, a number comparable to that in the human. However, the absence of KRT37 in the type I family and the discovery of type II KRT87 in sheep exemplify species-specific compositional differences in hair KRT genes. Phylogenetic analysis of hair KRT genes within type I and type II families in the sheep, cattle and human genomes revealed a high degree of consistency in their sequence conservation and grouping. However, there were differences in the fibre compartmentalisation and keratinisation zones for the expression of six ovine KRT genes compared with their human orthologs. Transcripts of three genes (KRT40, KRT82 and KRT84) were only present in the fibre cuticle. KRT32, KRT35 and KRT85 were expressed in both the cuticle and the fibre cortex. The remaining 11 genes (KRT31, KRT33A, KRT33B, KRT34, KRT36, KRT38-39, KRT81, KRT83 and KRT86-87) were expressed only in the cortex. Species-specific differences in the expressed keratin gene sets, their relative expression levels and compartmentalisation are discussed in the context of their underlying roles in wool and hair developmental programmes and the distinctive characteristics of the fibres produced.


Assuntos
Expressão Gênica/genética , Queratinas/classificação , Queratinas/genética , Ovinos/genética , Ovinos/metabolismo , Animais , Sequência de Bases/genética , Bovinos , DNA Complementar/genética , Folículo Piloso/metabolismo , Humanos , Queratinócitos/metabolismo , Queratinas Específicas do Cabelo/classificação , Queratinas Específicas do Cabelo/genética , Queratinas Tipo I/classificação , Queratinas Tipo I/genética , Queratinas Tipo II/classificação , Queratinas Tipo II/genética , Anotação de Sequência Molecular , Dados de Sequência Molecular , Filogenia , Homologia de Sequência do Ácido Nucleico , Pele/metabolismo , Lã/química , Lã/crescimento & desenvolvimento
6.
J Mammary Gland Biol Neoplasia ; 15(1): 101-12, 2010 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-20131087

RESUMO

It is well established that milk production of the dairy cow is a function of mammary epithelial cell (MEC) number and activity and that these factors can be influenced by diverse environmental influences and management practises (nutrition, milk frequency, photoperiod, udder health, hormonal and local effectors). Thus, understanding how the mammary gland is able to respond to these environmental cues provides a huge potential to enhance milk production of the dairy cow. In recent years our understanding of molecular events within the MEC underlying bovine lactation has been advanced through mammary microarray studies and will be further advanced through the recent availability of the bovine genome sequence. In addition, the potential of epigenetic regulation (non-sequence inheritable chemical changes in chromatin, such as DNA methylation and histone modifications, which affect gene expression) to manipulate mammary function is emerging. We propose that a substantial proportion of unexplained phenotypic variation in the dairy cow is due to epigenetic regulation. Heritability of epigenetic marks also highlights the potential to modify lactation performance of offspring. Understanding the response of the MEC (cell signaling pathways and epigenetic mechanisms) to external stimuli will be an important prerequisite to devising new technologies for maximising their activity and, hence, milk production in the dairy cow.


Assuntos
Bovinos/fisiologia , Epigênese Genética , Células Epiteliais/fisiologia , Lactação/fisiologia , Glândulas Mamárias Animais/fisiologia , Proteínas do Leite/metabolismo , Leite/metabolismo , Animais , Metilação de DNA , Indústria de Laticínios/métodos , Células Epiteliais/metabolismo , Feminino , Regulação da Expressão Gênica , Genótipo , Histonas/metabolismo , Lactação/genética , Glândulas Mamárias Animais/metabolismo , Proteínas do Leite/genética , Fenótipo
7.
Genome Biol ; 10(4): R43, 2009.
Artigo em Inglês | MEDLINE | ID: mdl-19393040

RESUMO

BACKGROUND: The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS: Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome. Intersection of these genes with 238 milk production quantitative trait loci curated from the literature decreased the search space for milk trait effectors by more than an order of magnitude. Genome location analysis revealed a tendency for milk protein genes to be clustered with other mammary genes. Using the genomes of a monotreme (platypus), a marsupial (opossum), and five placental mammals (bovine, human, dog, mice, rat), gene loss and duplication, phylogeny, sequence conservation, and evolution were examined. Compared with other genes in the bovine genome, milk and mammary genes are: more likely to be present in all mammals; more likely to be duplicated in therians; more highly conserved across Mammalia; and evolving more slowly along the bovine lineage. The most divergent proteins in milk were associated with nutritional and immunological components of milk, whereas highly conserved proteins were associated with secretory processes. CONCLUSIONS: Although both copy number and sequence variation contribute to the diversity of milk protein composition across species, our results suggest that this diversity is primarily due to other mechanisms. Our findings support the essentiality of milk to the survival of mammalian neonates and the establishment of milk secretory mechanisms more than 160 million years ago.


Assuntos
Bovinos/genética , Genoma/genética , Lactação/genética , Proteínas do Leite/genética , Animais , Mapeamento Cromossômico , Cromossomos de Mamíferos/genética , Biologia Computacional/métodos , Bases de Dados Genéticas , Evolução Molecular , Feminino , Humanos , Mamíferos/classificação , Mamíferos/genética , Glândulas Mamárias Animais/metabolismo , Leite/química , Proteínas do Leite/classificação , Filogenia , Locos de Características Quantitativas/genética
8.
Differentiation ; 77(3): 307-16, 2009 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-19272529

RESUMO

The catalogue of hair keratin intermediate filaments (KIFs) and keratin-associated proteins (KAPs) present in wool follicles is incomplete. The full coding sequences for three novel sheep KIFs (KRT27, KRT35 and KRT38) and one KAP (KRTAP4-3) were established in this study. Spatial expression patterns of these and other genes (KRT31, KRT85, KRTAP6-1 and trichohyalin) were determined by in situ hybridisation in wool follicles at synchronised stages of growth. Transcription proceeded in the order: trichohyalin, KRT27, KRT85, KRT35, KRT31, KRT38, KRTAP6-1 and KRTAP4-3, as determined by increasing distance of their expression zones from the germinal matrix in anagen follicles. Expression became gradually more restricted to the lower follicle during follicle regression (catagen), and ceased during dormancy (telogen). Some genes (KRT27, KRT31, KRT85 and KRTAP6-1), but not others, were expressed in cortical cells forming the brush-end, indicating specific requirements for the formation of this anchoring structure. The resumption of keratin expression was observed only in later stages of follicle reactivation (proanagen). KIF expression patterns in primary wool follicles showed general resemblance to their human homologues but with some unique features. Consistent differences in localisation between primary and secondary wool follicles were observed. Asymmetrical expression of KRT27, KRT31, KRT35, KRT85 and trichohyalin genes in secondary follicles were associated with bulb deflection and follicle curvature, suggesting a role in the determination of follicle and fibre morphology.


Assuntos
Regulação da Expressão Gênica , Folículo Piloso/metabolismo , Filamentos Intermediários/genética , Filamentos Intermediários/metabolismo , Queratinas , Ovinos/metabolismo , , Animais , Sequência de Bases , Perfilação da Expressão Gênica , Folículo Piloso/crescimento & desenvolvimento , Queratinas/genética , Queratinas/metabolismo , Dados de Sequência Molecular , RNA Mensageiro/metabolismo , Ovinos/genética
9.
BMC Genomics ; 8: 75, 2007 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-17362520

RESUMO

BACKGROUND: Cattle and other ruminants have evolved the ability to derive most of their metabolic energy requirement from otherwise indigestible plant matter through a symbiotic relationship with plant fibre degrading microbes within a specialised fermentation chamber, the rumen. The genetic changes underlying the evolution of the ruminant lifestyle are poorly understood. The BPI-like locus encodes several putative innate immune proteins, expressed predominantly in the oral cavity and airways, which are structurally related to Bactericidal/Permeability Increasing protein (BPI). We have previously reported the expression of variant BPI-like proteins in cattle (Biochim Biophys Acta 2002, 1579, 92-100). Characterisation of the BPI-like locus in cattle would lead to a better understanding of the role of the BPI-like proteins in cattle physiology RESULTS: We have sequenced and characterised a 722 kbp segment of BTA13 containing the bovine BPI-like protein locus. Nine of the 13 contiguous BPI-like genes in the locus in cattle are orthologous to genes in the human and mouse locus, and are thought to play a role in host defence. Phylogenetic analysis indicates the remaining four genes, which we have named BSP30A, BSP30B, BSP30C and BSP30D, appear to have arisen in cattle through a series of duplications. The transcripts of the four BSP30 genes are most abundant in tissues associated with the oral cavity and airways. BSP30C transcripts are also found in the abomasum. This, as well as the ratios of non-synonymous to synonymous differences between pairs of the BSP30 genes, is consistent with at least BSP30C having acquired a distinct function from the other BSP30 proteins and from its paralog in human and mouse, parotid secretory protein (PSP). CONCLUSION: The BPI-like locus in mammals appears to have evolved rapidly through multiple gene duplication events, and is thus a hot spot for genome evolution. It is possible that BSP30 gene duplication is a characteristic feature of ruminants and that the BSP30 proteins contribute to an aspect of ruminant-specific physiology.


Assuntos
Peptídeos Catiônicos Antimicrobianos/genética , Proteínas Sanguíneas/genética , Proteínas de Transporte/genética , Duplicação Gênica , Proteínas de Membrana/genética , Animais , Peptídeos Catiônicos Antimicrobianos/metabolismo , Proteínas Sanguíneas/metabolismo , Proteínas de Transporte/metabolismo , Bovinos , Evolução Molecular , Expressão Gênica , Humanos , Proteínas de Membrana/metabolismo , Camundongos , Modelos Moleculares , Filogenia , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico
10.
Genetics ; 160(4): 1587-97, 2002 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-11973312

RESUMO

Comparative maps between ruminant species and humans are increasingly important tools for the discovery of genes underlying economically important traits. In this article we present a primary linkage map of the deer genome derived from an interspecies hybrid between red deer (Cervus elaphus) and Père David's deer (Elaphurus davidianus). The map is approximately 2500 cM long and contains >600 markers including both evolutionary conserved type I markers and highly polymorphic type II markers (microsatellites). Comparative mapping by annotation and sequence similarity (COMPASS) was demonstrated to be a useful tool for mapping bovine and ovine ESTs in deer. Using marker order as a phylogenetic character and comparative map information from human, mouse, deer, cattle, and sheep, we reconstructed the karyotype of the ancestral Pecoran mammal and identified the chromosome rearrangements that have occurred in the sheep, cattle, and deer lineages. The deer map and interspecies hybrid pedigrees described here are a valuable resource for (1) predicting the location of orthologs to human genes in ruminants, (2) mapping QTL in farmed and wild deer populations, and (3) ruminant phylogenetic studies.


Assuntos
Mapeamento Cromossômico , Cervos/genética , Evolução Molecular , Genoma , Animais , Bovinos , Etiquetas de Sequências Expressas , Humanos , Repetições de Microssatélites , Ruminantes/genética
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