Complete mitochondrial genome of Oxya chinensis （Orthoptera, Acridoidea）

The complete sequence of Oxya chinensis （0. chinensis） mitochondrial genome is reported here. It is 15,443 bp in length and contains 75.9% A＋T. The protein-coding genes have a similar A＋T content （75.2%）. The initiation codon of the cytochrome oxidase subunit I gene in the mitochondrial genome of O. chinensis appears to be ATC, instead of the tetranucleotides that have been reported in Locusta migratoria （L migratoria） mitochondrial genome. The sizes of the large and small ribosomal RNA genes are 1319 and 850 bp, respectively. The transfer RNA genes have been modeled and showed strong resemblance to the dipteran transfer RNAs, and all anticodons are identical to those of dipteran. The A＋T-rich region is 562 bp, shorter than that of other known Orthoptera insects. The six conserved domains were identified within the A＋T-rich region by comparing its sequence with those of other grasshoppers. The result of phylogenetic analysis based on the dataset containing 12 concatenated protein sequences confirms the close relation-ship of O. chinensis with L migratoria.     

Expression of two soybean resistance gene candidates shows divergence of paralogous single-copy genes

The cloning of several plant genes directly involved in triggering a disease resistance response has shown that numerous resistance genes in the nucleotide binding site (NBS)/leucine-rich repeat (LRR) class have similar conserved amino acid sequences. In this study, we used a short soybean DNA sequence, previously cloned based on its conserved NBS, as a probe to identify full-length resistance gene candidates. Two homologous, but genetically independent genes were identified. One gene maps to the soybean molecular linkage group (MLG) F and a second is coded on MLG E. The first gene contains a 3,279 nucleotide open reading frame (ORF) sequence and possesses all the functional motifs characteristic of previously cloned NBS/LRR resistance genes. The N-terminal sequence of the deduced gene product is highly characteristic of other resistance genes in the subgroup of NBS/LRR genes which show homology to the Toll/Interleukin-1 receptor genes. The C-terminal region is somewhat more divergent as seen in other cloned disease resistance genes. This region of the F-linked gene contains an LRR region that is characterized by two alternatively spliced products which produce gene products with either a four-repeat or a ten-repeat LRR. The second cloned gene that maps to soybean MLG E contains 1,565 nucleotides of ORF in the N-terminal domain. Despite strong homology, however, the 3′ region of this gene contains several in-frame stop codons and apparent frame shifts compared to the F-linked gene, suggesting that its functionality as a disease resistance gene is questionable. These two disease resistance gene candidates are shown to be closely related to one another and to the members of the NBS/LRR class of disease resistance genes. Received: 29 November 1999 / Accepted: 22 December 1999     

Cloning and characterization of nanos gene in silkworm Bombyx mori

Gene nanos is a maternal posterior group gene required for normal development of abdominal segments and the germ line in Drosophila. Expression of nanos-related genes is associated with the germ line in a broad variety of other taxa. In this study, the 5＇-RACE method and the in silico cloning method are used to isolate the new nanos-like gene of Bombyx mor/and the gene obtained is analyzed with bioinformatics tools. The putative protein is expressed in Escherichia coli and the antiserum has been produced in New Zealand white rabbits. The result shows that the nanos cDNA is 1,913 bp in full length and contains a 954 bp open reading frame. The deduced protein has 317 amino acid residues, with a predicted molecular weight of 35 kDa, isoelectric point of 5.38, and contains a conserved nanos RNA binding domain. The conserved region of the deduced protein shares 73% homology with the nanos protein conserved region of Honeybee （Apis mellifera）. This gene has been registered in the GenBank under the accession number EF647589. One encoding sequence of the nanos fragment has been successfully expressed in E. coli. Western blotting analysis indicates that homemade antiserum can specifically detect nanos protein expressed in prokaryotic cells.     

The Mitochondrial Genome of Raphanus sativus and Gene Evolution of Cruciferous Mitochondrial Types

To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome of Raphanus sativus (sat) was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorga-nization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype), together with six other re-ported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis (a representative gymnosperm), the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions (indels), have resulted in the non- conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.     

The complete mitochondrial genome sequence of Geisha distinctissima （Hemiptera： Flatidae） and comparison with other hemipteran insects

The complete nucleotide sequence of the mitochondrial genome （mitogenome） of Geisha distinctissima （Hemiptera： Flatidae） has been determined in this study. The genome is a circular molecule of 15,971 bp with a total A＋T content of 75.1%. The gene content, order, and structure are consistent with the Drosophila yakuba genome structure and the hypothesized ancestral arthro- pod genome arrangement. All 13 protein-coding genes are observed to have a putative, inframe ATR methionine or ATT isoleucine codons as start signals. Canonical TAA and TAG termination codons are found in nine protein-coding genes, and the remaining four （cox1, atp6, cox3, and nad4） have incomplete termination codons. The anticodons of all transfer RNA （tRNAs） are identical to those observed in D. yakuba and Philaenus spumarius, and can be folded in the form of a typical clover-leaf structure except for tRNASer（AGN）. The major non-coding region （the A ＋ T-rich region or putative control region） between the small ribosomal subunit and the tRNAne gene includes two sets of repeat regions. The first repeat region consists of a direct 152-bp repetitive unit located near the srRNA gene end, and the second repeat region is composed of a direct repeat unit of 19 bp located toward tRNAIle gene. Comparisons of gene variability across the order suggest that the gene content and arrangement of G. distinctissima mitogenome are similar to other hemipteran insects.     

The first mitochondrial genome for the butterfly family Riodinidae(Abisara fylloides) and its systematic implications

The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides, the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A. fylloides is 15 301 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22transfer RNA genes and a 423 bp A+T-rich region. The gene content, orientation and order are identical to the majority of other lepidopteran insects. Phylogenetic reconstruction was conducted using the concatenated 13 protein-coding gene(PCG) sequences of19 available butterfly species covering all the five butterfly families(Papilionidae, Nymphalidae, Peridae, Lycaenidae and Riodinidae). Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae,which was standing as the sister of Nymphalidae. In addition, we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon.     

Identification and analyses of miRNA genes in allotetraploid Gossypium hirsutum fiber cells based on the sequenced diploid G. raimondii genome

The plant genome possesses a large number of microRNAs（miRNAs）mainly 21-24 nucleotides in length.They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle.Here we sequenced and analyzed～10 million non-coding RNAs（ncRNAs）derived from fiber tissue of the allotetraploid cotton（Gossypium hirsutum）1 days post-anthesis using ncRNA-seq technology.In terms of distinct reads,24 nt ncRNA is by far the dominant species,followed by 21 nt and 23 nt ncRNAs. Using ab initio prediction,we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D₅ genome of the diploid cotton G.raimondii.Of all the 562 predicted miRNAs,22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species.Nucleotide bias analysis showed that the 9th and 1 st positions were significantly conserved among different types of miRNA genes.Among the 463 putative miRNA target genes,most significant up/down-regulation occurred in 10-20 days post-anthesis,indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development.The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.     

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis(Aves,Passeridae) complete mitochondrial genome

In this study,both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome(KC836121).The results showed that the complete mitochondrial genome of P.ruficollis is 16909 bp in length with 55.0%A+T content,harboring the typical 37 genes.The mitogenome had the same gene order with that of Podoces hendersoni.All protein coding genes started with ATG codon,except ND3 with GTG.For the stop codon usage,most genes terminate with codons TAA or TAG,but ND5 terminated with AGA,while ND1 and COI genes with AGG,and both the genes COIII and ND4 have an incomplete termination codon(T).The secondary structures of 22 tRNA genes were also predicted,showing that all tRNAs can form typical clover-leaf secondary structures,except for the tRNASer(AGN)which loses the DHU arm,while tRNAPhe harbor an extra nucleotide inserted in the TψC arm.The predicted secondary structures of 12S rRNA and16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively.The control region of P.ruficollis with the length of 1 305 bp was located between tRNAGlu and tRNAPhe,and typical domains of which could be found as other bird groups.Using the data from 13 mitochondrial protein-coding genes,results of a final phylogenetic analysis strongly supports the traditional view that P.ruficollis is closely related with Passeridae and Fringillidae.     

A Mitochondrial Genome Sequence of the Tibetan Antelope （ Pantholops hodgsonii ）

To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis ames and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii （16,498 bp） revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. ames and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. ames and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. ames is about 2.25 million years ago. Eutther analysis on natural selection indicated that the COXI （cytochrome c oxidase subunit I） gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.     

Structural and Expressional Variations of the Mitochondrial Genome Conferring the Wild Abortive Type of Cytoplasmic Male Sterility in Rice

The so-called ＂wild abortive＂ （WA） type of cytoplasmic male sterility （CMS） derived from a wild rice species Oryza rufipogon has been extensively used for hybrid rice breeding. However, extensive analysis of the structure of the related mitochondrial genome has not been reported, and the CMS-associated gene（s） remain unknown. In this study, we exploited a mitochondrial genome-wide strategy to examine the structural and expressional variations in the mitochondrial genome conferring the CMS. The entire mitochondriai genomes of a CMS-WA line and two normal fertile rice lines were amplified by Long-polymerase chain reaction into tilling fragments of up to 15.2 kb. Restriction and DNA blotting analyses of these fragments revealed that structural variations occurred in several regions in the WA mitochondrial genome, as compared to those of the fertile lines. All of the amplified fragments covering the entire mitochondrial genome were used as RNA blot probes to examine the mitochondriai expression profile among the CMS-WA and fertile lines. As a result, only two mRNAs were found to be differentially expressed between the CMS-WA and the fertile lines, which were detected by a probe containing the nad5 and orf153 genes and the other having the ribosomal protein gene rpl5, respectively. These mRNAs are proposed to be the candidates for further identification and functional studies of the CMS gene.     

Molecular characterization and expression analysis of Triticum aestivum squamosa-promoter binding protein-box genes involved in ear development

Wheat(Triticum aestivum L.) is one of the most important crops in the world. Squamosa-promoter binding protein(SBP)-box genes play a critical role in regulating flower and fruit development. In this study, 10 novel SBP-box genes(TaSPL genes) were isolated from wheat((Triticum aestivum L.) cultivar Yanzhan 4110). Phylogenetic analysis classified the TaSPL genes into five groups(G1–G5). The motif combinations and expression patterns of the TaSPL genes varied among the five groups with each having own distinctive characteristics: TaSPL20/21 in G1 and TaSPL17 in G2 mainly expressed in the shoot apical meristem and the young ear, and their expression levels responded to development of the ear; TaSPL6/15 belonging to G3 were upregulated and TaSPL1/23 in G4 were downregulated during grain development; the gene in G5(TaSPL3) expressed constitutively. Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions.On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP-box genes have a wide range of functions. The results also suggest a potential role for wheat SBP-box genes in ear development.This study provides a significant beginning of functional analysis of SBP-box genes in wheat.     

The complete mitochondrial genome and phylogenetic analysis of Nyctereutes procyonoides

The complete mitochondrial genome sequence of the raccoon dog (Nyctereutes procyonoides) was determined by using the long and accurate polymerase chain reaction. The entire mitochondrial genome sequence is 16,713 bp in length contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 control region. Most mitochondrial genes are encoded on the H strand, except for the ND6 gene and 8 tRNA genes. The base compositions of mitochondrial genomes present clearly A–T skew. All the transfer RNA genes can be folded into the typical cloverleaf-shaped structure except tRNA-Ser (AGY), which lacks the dihydrouridine arm. Protein-coding genes mainly initiate with ATG and terminate with TAA. Some reading frame intervals and overlaps are found in the mitochondrial genome. The control region can be divided into three domains: the extended termination associated sequences (ETASs) domain, the central conserved domain and the conserved sequence blocks (CSBs) domain. Three conserved sequence blocks (CSBs) and one extended termination associated sequences (ETAS-1) is found in the control region. The phylogenetic analysis based on the concatenated data set of 14 genes in the mitochondrial genome of Canidae shows that the raccoon dog has close phylogenetic position with the red fox (Vulpes vulpes) and they constitute a clade which has an equil evolutionary position with the clade formed by the genera Canis and Cuon.