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The grain Chenopodium quinoa Willd. is the main traditional food of Inca aboriginal, which was a native grain in South American Andes Mountains, the edible and cultivation history of which has been more than five thousand years. In this study, we sequenced the complete chloroplast genome of C. quinoa on the Illumina platform by shotgun genome skimming method. The complete chloroplast genome of C. quinoa was 152,087 bp in length with the GC content 37.2%, which was comprised of a large single copy (LSC) region of 83,570 bp, a small single copy (SSC) region of 18,107 bp, and a pair of inverted repeats (IRA/IRB) of 25,205 bp. The chloroplast genome encoded 133 genes including 88 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis constructed using the maximum likelihood (ML) method strongly supported the monophyly of each genus in the family Chenopodiaceae, and the genus Chenopodium is sister to Spinacia as a cluster, which closely grouped to Dysphania.
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The complete mitochondrial genome (mitogenome) of golden pheasant Chrysolophus pictus from North China was sequenced by the shotgun genome skimming methods. The mitogenome of C. pictus was 16,678 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one non-coding control region (D-loop). Its overall base composition was 30.4% A, 24.8% T, 31.2% C and 13.6% G. All protein-coding genes had a typical ATG initiation codon except COX1 with GTG and terminated with a TAN codon, whereas COX1 terminated with a codon of AGG, COX3, ND2 and ND4 terminated with a single T. The ML phylogenetic tree constructed using 13 protein-coding genes showed that Chrysolophus species formed a monophyletic group, which was sister to the clade clustered by the two genera Crossoptilon and Lophura.
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We sequenced the complete mitochondrial genome (mitogenome) of Mustela sibirica in China by the shotgun genome skimming methods. The mitogenome of M. sibirica is 16,558bp in length with the base composition of 32.9% A, 27.3% T, 26.0% C, and 13.9% G, and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one non-coding control region. The 13 PCGs use ATG as initiation codons except ND3, ND5 and ND2 which initiate with codons ATA and ATT, respectively. Four (COX3, ND1, ND2 and ND4) of the 13 PCGs terminate with a single T- -, and the remainder with a TAA termination codon except ND3 and CYT B using TA- and AGA as termination codon. The phylogenetic tree based on 13 protein-coding genes indicated that M. sibirica is sister to the clade grouped with three species M. nigripes, M. eversmannii, and M. putorius, and Mustelinae species formed a monophyletic group, which is close to the Lutrinae clade within Mustelidae.
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Flavonoids are a group of secondary metabolites found in plants. They have many pharmacological functions and play an important role in Chinese sumac( Rhus chinensis),which is a well-known traditional Chinese medicinal plant. Chalcone isomerase( CHI,EC 5. 5. 1. 6) is one of the key enzymes in the flavonoids biosynthesis pathway. In this paper,the full-length c DNA sequence encoding the chalcone isomerase from R. chinensis( designated as Rc CHI) was cloned by RT-PCR and rapid-amplification of c DNA Ends( RACE). The Rc CHI c DNA sequence was 1 058 bp and the open reading frame( ORF) was 738 bp. The ORF predicted to encode a 245-amino acid polypeptide. Rc CHI gene contained an intron and two exons. The sequence alignments revealed Rc CHI shared47. 1%-71. 6% identity with the homologues in other plants. Real-time PCR analysis showed that the total flavonoid levels were positively correlated with tissue-specific expressions of Rc CHI mRNA in different tissues. The recombinant protein was successfully expressed in an Escherichia coli strain with the p GEX-6 P-1 vector. In this paper,the CHI gene was cloned and characterized in the family of Anacardiaceae and will help us to obtain better knowledge of the flavonoids biosynthesis of the flavonoid compounds in R. chinensis.
Asunto(s)
Flavonoides/biosíntesis , Liasas Intramoleculares/genética , Rhus/enzimología , Clonación Molecular , ADN Complementario , Plantas Medicinales/enzimología , Plantas Medicinales/genética , Rhus/genéticaRESUMEN
We sequenced the complete mitochondrial genome of the Chinese Rhus gall aphid Meitanaphis microgallis (Hemiptera: Aphididae: Eriosomatinae: Fordini) by the genome skimming method on an Illunima platform. The assembled mitogenome is 16,191 bp in length with a very high A + T content of 84.3%. This genome consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. All the protein-coding genes have a typical ATN initiation codon and TAA termination codon except COX1 and ND4 with a single T as stop codon. The tRNAs ranged in size from 59 to 77 bp and formed a clover-leaf secondary structure except tRNA-Ser (AGN). We constructed the phylogenetic relationship of Fordini aphids including all the Rhus gall aphids, and the ML tree showed that M. microgallis grouped with M. elongallis as its sister group.
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We sequenced the complete mitochondrial genome (mitogenome) of Siberian Roe Deer, Capreolus pygargus, in China by the shotgun genome-skimming methods. The mitogenome of C. pygargus is totally 16,353 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The sequence has a higher A + T content of 63.4% than G + C 36.6% and with a base composition of 33.4% A, 23.2% C, 13.4% G, and 30.0% T. All of the 13 PCGs initiate a typical ATN codon except Nd4L with GTG. Six PCGs terminate with a TAA codon, while Cyt b, Atp8, and Nd1 terminate with AGA, TAG, and TA-, respectively. Whereas, Cox3, Nd2, Nd3, and Nd4 terminate with a single T-. The phylogenetic trees of the subfamily Capreolinae with 13 PCGs indicated that Capreolus species were well-supported as a monophyletic group, which is sister to the clade of Hydropotes with well-support.
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The complete mitochondrial genome (mitogenome) of black stork Ciconia nigra from North China was sequenced by shotgun genome-skimming method. The mitogenome of C. nigra was 17,787 bp in length and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs, and one non-coding control region (D-loop). All protein-coding genes initiate with ATG codon except for ND2, ND3, and COX1, which uses ATA, ATC, and GTG as their initiation codons, respectively. The termination codon of protein-coding genes shows rich diversity with six termination codons (TAA, AGG, AGA, TAG, T, and A). The phylogenetic trees based on 13 protein-coding genes showed that Ciconia formed a monophyletic group, which was sister to the clade clustered by Threskiorothidae species.
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The complete mitochondrial genome (mitogenome) of the leopard cat Prionailurus bengalensis in China was sequenced using the shotgun genome-skimming method. The mitogenome of P. bengalensis is totally 17,006 bp in length with a higher A + T content of 60.4% than that of G + C and consists of 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region. All the PCGs initiate with a typical ATN codon and terminate with a TAA codon except for the four PCGs (COX1, ND2, ND3, and ND4) terminating with a single T-and one gene CYT B with AGA as stop codon. Most of the tRNA genes have a clover-leaf secondary structure except for tRNAS (AGN), which loses a dihydrouridine (DHU) arm. The ML phylogenetic tree showed that P. viverrinus nested in the group of P. bengalensis individuals, which is close to the clade clustered by the two genera Otocolobus and Felis.
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We sequenced the complete mitochondrial genome (mitogenome) for the North American Rhus gall aphid species Melaphis rhois. The mitogenome is 15,436 bp in length with a high A + T content of 82.7%, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Its gene order is identical to that of the eastern Asian species Schlechtendalia chinensis. All protein-coding genes start with a typical ATN codon and terminate with a TAA codon except COI and ND4 by a single T residue. All the tRNAs except tRNACys formed a clover-leaf secondary structure. The mitogenome phylogeny of Aphididae suggests that M. rhois is most closely related to the eastern Asian Rhus gall aphid S. chinensis with the present sampling scheme.
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We sequenced the first complete mitochondrial genome for the aphid subfamily, Eriosomatinae, from a Rhus gall aphid, Schlechtendalia chinensis. The mitogenome of S. chinensis is 16,047 bp in length with a high A + T content of 84.2% and consists of 13 protein-coding genes, 24 tRNA genes including two extra tRNAPhe , two rRNA genes, a repeat region, and a control region. All protein-coding genes have a typical ATN initiation codon and TAA termination codon except COI and ND4, which terminate with a single T. All 24 tRNAs have the expected clover-leaf secondary structure and range in size from 62 to 73 bp. The lengths of rrnL and rrnS genes are 1274 and 772 bp, respectively. The repeat region is 335 bp and is uncommon among known aphid sequences for starting with a tRNAPhe . The control region is 705 bp in length and is located between rrnS and tRNAIle . We present a phylogeny of mitogenomes showing that S. chinensis is sister to Aphidinae.
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The mtDNA Cyt b genes (432 bp) were sequenced for 16 individuals of Oxya agavisa from 7 Chinese region, 3 other relative species (O. japonica, O. chinensis and O. intricata), and two outgroup species (Pseudomorphacris hollisi and Tetrix japonica). In the obtained sequences of O. agavisa, A% + T% was about 71.0% and 9 polymorphic nucleotide sites were observed (about 2.08%), among which no transversions were observed and only one substitution resulted in the variation of amino acid. In the case of 3 other species of Oxya, A% + T% was about 72.5% (O. chinensis) and 70% (O. japonica and O. intricata), respectively. A% + T% in the third site was much higher than the other two sites in all the analyzed Oxya species (O. agavisa, 88.3%; O. chinensis, 92.4%; O. japonica, 86.8%; O. intricata, 89.5%). Six haplotypes of O. agavisa were compared with the 3 other Oxya species and 73 polymorphic nucleotide sites were examined (about 16.9%) in all. Phylogenetic tree was constructed with the Neighbor-Joining methods using P. hollisi and T. japonica as outgroups and the confidence of nodes in the tree was evaluated by Bootstrap(1000 replicates). The NJ tree showed that different haplotypes of O. agavisa clustered together, but no clear relationships between haplotypes and the geographic regions would be inferred. The population from Mount Wuyi belongs to the peculiar group and is relatively distant to other populations. In addition, the NJ tree showed that O. agavisa was closer to O. japonica and O. chinensis closer to O. intricata, which was different from the previous results of morphologic, chromosome karyotype and bands. The relationships among different species of Oxya still need to be further clarified.
Asunto(s)
Grupo Citocromo b/genética , ADN Mitocondrial , Saltamontes/genética , Animales , Secuencia de Bases , ADN Complementario , ADN Mitocondrial/análisis , Saltamontes/clasificación , Datos de Secuencia Molecular , Oryza , Filogenia , Análisis de Secuencia de ADN , Homología de Secuencia de Ácido NucleicoRESUMEN
The mtDNA Cyt b sequences (432 bp) were analyzed in 10 individuals from 8 different families of Acridoidea in China. The homologous sequences were compared, the used frequency of nucleotide was calculated and the molecular phylogenetic tree constructed by Neighbor-Joining method using T. japonica as outgroup. The confidence of nodes in the trees was evaluated by bootstrap (1000 replicates). These sequences were the middle part of Cyt b gene, and in the obtained sequences, A% + T% was about 70.4% and G% + C% only 29.6%. The sequence data revealed considerable variation in 177 nucleotide sites (about 41.0%) among the analyzed individuals from 8 different families. From every amino acid codon, A% + T% in the third site was higher (86.6%) than the other two sites and lower than other insects in the corresponding region. The NJ tree suggested that 11 individuals from the 8 families clustered in 4 groups, among which Gomphoceridae and Pamphagidae firstly clustered and then together with Arcypteridae and Acrididae to form group I; Cluster II was made of three species from Catantopidae, O. japonica, O. chinensis and O. intricata; Pyrgmorphidae and Oedipodidae formed group III and Chrotogonidae single as cluster IV, respectively. The phylogenetic relationships of the 8 families was: Chrotogonidae-->Pyrgomorphidae and Oedipodidae-->Catantopidae-->Acrididae-->Arcypteridae-->Gomphoceridae and Pamphagidae, which is little different from the morphological results.
