Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

玉米的单倍体育种及基因转化的研究

玉米的单倍体育种，是利用花药培养或孤雌生殖产生单倍体后，进行人工或自然加倍，迅速获得稳定的新品种的育种方法。单倍体育种可以缩短育种时间，单倍体培养体系如果作为转基因的受体，可保证外源基因在后代中稳定遗传，而不发生分离。因此，玉米单倍体育种无论在实践中还是在理论研究方面都具有重大的意义。 本文针对玉米花药培养中长期以来未能解决的诱导频率低、基因型之间差异大、小苗移栽不容易成活等问题，重点探讨了各种因素对玉米花药培养的影响。结果表明：不同基因型之间的诱导频率差异明显，杂交种的诱导频率比纯系高，并选择出诱导频率高达20%的材料“中0198”;接种时花药中的花粉处于单核中期时，其诱导频率最高;采用液体培养基比采用固体培养基诱导频率提高一倍;培养基中加入0.5%的活性炭，可使诱导频率由5.25%提高到9.35%;15%的蔗糖浓度对玉米的花药培养是最适宜的，培养2周后，将培养基的蔗糖浓度从15%调整为10%，将明显提高诱导频率;培养基中高浓度的KT和低浓度的BA有利于诱导体细胞胚的发生，而低浓度的KT和高浓度的BA有利于诱导芽的发生;接种前将花药在4℃条件下进行低温预处理，可将诱导频率从3.13%提高到11.71%;培养基中添加2 mg/l的多效唑，可有效地促进小苗的生根;再生植株于冬季拿到海南种植，可明显提高移栽的成活率。 在玉米孤雌生殖的实验中，将未受粉的玉米雌穗接种在成份为N6 + 2,4-D 1mg/L + NAA 1mg/L + BA 1mg/L + CH 200mg/L + colchicine 2 mg/L + sucrose 5% + agar 0.7% 的培养基上。第一轮实验共接种了三个材料的26个雌穗（约3900个未受精的子房）。每种材料均有单性结实，诱导频率由高到低分别3.06%，2.29%，1.90%。直接获得了5株再生植株，通过染色体检查，发现其中3株为单倍体（n=10），另外2株为二倍体。移栽到土壤中后，有4株成活，其中一株二倍体植株能够正常开花、结实。得到的种子播种于实验田中，表现整齐一致，有纯系的特征，而且出现了2株白化苗。通过石蜡切片初步观察了孤雌生殖的胚胎发生过程，发现胚胎发生是从胚囊里的单倍体细胞起源的。第二、三轮实验又接种了10个基因型的玉米材料，证实了上述结果。 外源基因转导是利用生物技术进行玉米育种的一个有效途径。本文首次尝试了用离体子房注射法对玉米进行基因转化。首先构建了含有开花促进因子基因FPF1及植物选择标记抗除草剂基因pat的植物表达载体pFBR，采用离体注射培养法，取授粉24小时后的玉米雌穗，剥去苞叶，在超净工作台进行微量注射，然后切成小块接种在培养基上，在光照培养箱内培养，3-4周可直接获得种子或小植株。种子萌发后进行植株抗性筛选和分子检测，共注射了3个品种的47个雌穗（约16450个子房）得到再生植株109株，其中经PPT筛选有抗性的植株为23株，占再生植株的21.1%。经PCR检测，13株植株有阳性反应。但Southern杂交检测有杂带出现。出现杂带的原因、RNA水平的分子检测、转基因后代T1代的分子检测和早开花农艺性状的观察，由于时间关系没有完成，还需要进一步的实验。实验初步证明了离体子房注射法对玉米进行基因转化的可行性，而且与田间注射法相比，此方法具有省力省时，容易控制污染，转化效率提高的优点, 克服了玉米培养再生植株受基因型限制的困境, 将为玉米分子育种的基因工程提供更易行的手段。 同时，也为子房较大的其它植物的基因转化提供了方法。

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Identification of Sarcocystis hominis-like (Protozoa : Sarcocystidae) cyst in water buffalo (Bubalus bubalis) based on 18S rRNA gene sequences

DNA templates were extracted from isolates of Sarcocystis hominis-like cysts collected from cattle and water buffalo, as well as from Sarcocystis fusiformis cysts and Sarcocystis suihominis cysts. The 18S rRNA genes were amplified using DNA from a single

Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Thirteen restriction endonucleases were used to investigate nucleotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of

Identification and molecular evolution of cow CENP-A gene family

The centromere protein A (CENP-A), a histone H3-like protein, provides an essential role for chromosomal segregation during mitosis and meiosis. In this study we identified ten new CENP-A-like genes (excluding the original CENP-A gene) in cow by searching

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene, GlTop 2 was identified. It is a single copy gene with a 4476 by long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a similar to 100 as longer central domain; a similar to 200 as shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the "amitochondriate" G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G. lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.

Identification of a Giardia krr1 homolog gene and the secondarily anucleolate condition of Giaridia lamblia

Giaridia lamblia was long considered to be one of the most primitive eukaryotes and to lie close to the transition between prokaryotes and eukaryotes, but several supporting features, such as lack of mitochondrion and Golgi, have been challenged recently. It was also reported previously that G. lamblia lacked nucleolus, which is the site of pre-rRNA processing and ribosomal assembling in the other eukaryotic cells. Here, we report the identification of the yeast homolog gene, krr1, in the anucleolate eukaryote, G. lamblia. The krr1 gene, encoding one of the pre-rRNA processing proteins in yeast, is actively transcribed in G. lamblia. The deduced protein sequence of G. lamblia krr1 is highly similar to yeast KRR1p that contains a single-KH domain. Our database searches indicated that krr1 genes actually present in diverse eukaryotes and also seem to present in Archaea. However, only the eukaryotic homologs, including that of G. lamblia, have the single-KH domain, which contains the conserved motif KR(K)R. Fibrillarin, another important pre-rRNA processing protein has also been identified previously in G. lamblia. Moreover, our database search shows that nearly half of the other nucleolus-localized protein genes of eukaryotic cells also have their homologs in Giardia. Therefore, we suggest that a common mechanism of pre-RNA processing may operate in the anucleolate eukaryote G. lamblia and in the other eukaryotes and that like the case of "lack of mitochondrion," "lack of nucleolus" may not be a primitive feature, but a secondarily evolutionary condition of the parasite.

Identification and association of the single nucleotide polymorphisms in calpain3 (CAPN3) gene with carcass traits in chickens

Background: The aim of this study is to screen single nucleotide polymorphisms (SNP) of chicken Calpain3 (CAPN3) gene and to analyze the potential association between CAPN3 gene polymorphisms and carcass traits in chickens. We screened CAPN3 single nucleo

Identification of a novel gene K23 over-expressed in fish cross-subfamily cloned embryos

A novel gene-K23, differentially expressed in cross-subfamily cloned embryos, was isolated by RACE-PCR technique. It had 2580 base pairs (bp) in length, with a 1,425 bp open reading frame (ORF) encoding a putative protein of 474 amino acids (aa). Bioinformatic analysis indicated that K23 had 22 phosphorylation sites, but it had no signal peptides. Developmental expression analysis in zebrafish showed that K23 transcripts were maternally expressed in ovum and the amount of K23 transcripts increased gradually from zygote to pharyngula period. Subcellular localization analysis revealed that K23 protein was homogeneously distributed both in nuclei and cytoplasm. Taken together, our findings indicate that K23 gene is a novel gene differentially expressed in fish cross-subfamily cloned embryos.

Identification of an additional two-cysteine containing type I interferon in rainbow trout Oncorhynchus mykiss provides evidence of a major gene duplication event within this gene family in teleosts

Multiple type I interferons (IFNs) have recently been identified in salmonids, containing two or four conserved cysteines. In this work, a novel two-cysteine containing (2C) IFN gene was identified in rainbow trout. This novel trout IFN gene (termed IFN5) formed a phylogenetic group that is distinct from the other three salmonid IFN groups sequenced to date and had a close evolutionary relationship with IFNs from advanced fish species. Our data demonstrate that two subgroups are apparent within each of the 2C and 4C type I IFNs, an evolutionary outcome possibly due to two rounds of genome duplication events that have occurred within teleosts. We have examined gene expression of the trout 2C type I IFN in cultured cells following stimulation with lipopolysaccharide, phytohaemagglutinin, polyI:C or recombinant IFN, or after transfection with polyI:C. The kinetics of gene expression was also studied after viral infection. Analysis of the regulatory elements in the IFN promoter region predicted several binding sites for key transcription factors that potentially play an important role in mediating IFN5 gene expression.