Complete DNA Sequence Research Articles

The complete chloroplast genome sequence of Angelica Tsinlingensis (Apioideae)

Angelica tsinlingensis is endemic in Shaanxi province (China), and is used as Angelica sinensis in folk. Owing to important medicinal value, wild A. sinensis has been over-exploited and become quite rare in China during over 2000 years. Angelica sensu lato (s.l.; Apiaceae subfamily Apioideae) is a taxonomically complex and controversial group, and A. tsinlingensis is clearly different from members of the Angelica s.s. clade with the morphological and molecular results. The complete chloroplast DNA sequence of A. tsinlingensis (GenBank accession number: MF924726) was determined in our study. The size of chloroplast genome of A. tsinlingensis is 147,104 bp, including a large single-copy (LSC) region of 93376 bp and a small single-copy (SSC) region of 17,574 bp separated by a pair of identical inverted repeat regions (IRs) of 18,077 bp each. A total of 125 genes were successfully annotated containing 83 protein-coding genes, 34 tRNA genes and 8 rRNA genes. GC content of IRs region is the highest (44.5%). The result of Phylogenomic analysis supports the difference of A. tsinlingensis from Angelica s.s. clade.

The complete mitochondrial DNA sequence from Kazachstania sinensis reveals a general +1C frameshift mechanism in CTGY codons.

The complete mitochondrial DNA (mtDNA) sequence from Kazachstania sinensis was analysed and compared to mtDNA from related yeasts. It contained the same set of genes; however, it only contained 23 tRNAs, as the trnR2 gene was absent. Most of the 12 introns within cox1, cob and rnl genes were inserted in the same sites as in other yeasts; however, two introns in rnl were in unusual positions. Traits such as gene order and GC cluster number were more related to Saccharomyces than to the other Kazachstania or linked clades. The most exceptional feature was the +1 frameshift in cox3, atp6 and cob open reading frames that was also found in other Kazachstania, Nakaseomyces delphensis and Candida glabrata. Comparison of DNA and protein sequences revealed the universal sites of +1C frameshifts were either CTGT or CTGC sequences. Moreover, an A→G substitution was found at position 37 in the anticodon stem loop tRNA gene for cysteine in all species with frameshifts but not in other sibling yeasts. This substitution allowed strong Watson-Crick base-pairing between an unmodified G (ACG) and the skipped C in the CTGY, leading to this quadruplet being read as cysteine.

Species composition of the genus Scombrops (Teleostei, Scombropidae) in the waters around the Japanese Archipelago: detection of a cryptic species

Current literature states that family Scombropidae consists of a single genus Scombrops comprising three species worldwide, with two of them, Scombrops boops and Scombrops gilberti, distributed in the waters around the Japanese Archipelago. Although these two scombropids are commercially important species, little is known about the ecology of these fishes. It is difficult to discriminate between these two species based on external characteristics because of their morphological similarity. Here, we report two different morphotypes characterized by the relative growth between the otolith size and the standard length (SL) of the scombropid specimens caught in southern waters off Kyushu Island, Japan, and show the genetic relationship between the morphotypes by means of phylogenetic analyses using complete DNA sequences of the cytochrome b gene. The relationship between otolith weight and SL was significantly different between specimens < 505 mm SL and those > 550 mm SL. Phylogenetic analysis demonstrated that the sequences from these scombropid specimens formed three clades: two corresponded to S. boops and S. gilberti, while the third did not correspond to any sequence recorded in databases, suggesting that these specimens are undescribed scombropid species. Almost all the specimens with SL < 505 mm (n = 76) were identified as S. boops, and only nine as S. gilberti. On the other hand, almost all the specimens with SL > 550 mm (n = 41) fell in the unidentified group except for four specimens, whose sequences were identical to that of S. boops.

Transcriptome, expression, and activity analyses reveal a vital heat shock protein 70 in the stress response of stony coral Pocillopora damicornis.

Coral bleaching occurs worldwide with increasing frequencies and intensities, which is caused by the stress response of stony coral to environmental change, especially increased sea surface temperature. In the present study, transcriptome, expression, and activity analyses were employed to illustrate the underlying molecular mechanisms of heat shock protein 70 (HSP70) in the stress response of coral to environmental changes. The domain analyses of assembled transcripts revealed 30 HSP70 gene contigs in stony coral Pocillopora damicornis. One crucial HSP70 (PdHSP70) was observed, whose expressions were induced by bothelevated temperature and ammonium after expression difference analysis. The complete complementary DNA (cDNA) sequence of PdHSP70 was identified, which encoded a polypeptide of 650 amino acids with a molecular weight of 71.93kDa. The deduced amino acid sequence of PdHSP70 contained a HSP70 domain (from Pro8 to Gly616), and it shared the highest similarity (95%) with HSP70 from Stylophora pistillata. The expression level of PdHSP70 gene increased significantly at 12h, and returned to the initial level at 24h after the stress of high temperature (32°C). The cDNA fragment encoding the mature peptide of PdHSP70 was recombined and expressed in the prokaryotic expression system. The ATPase activity of recombinant PdHSP70 protein was determined, and it did not change significantly in a wide range of temperature from 25 to 40°C. These results collectively suggested that PdHSP70 was a vital heat shock protein 70 in the stony coral P. damicornis, whose mRNA expression could be induced by diverse environmental stress and whose activity could remain stable under heat stress. PdHSP70 might be involved in the regulation of the bleaching owing to heat stress in the stony coral P. damicornis.

Organellar genome assembly methods and comparative analysis of horticultural plants

Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows–Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, Salix suchowensis, and a fruit tree, Ziziphus jujuba, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants.

Identification of a novel compound heterozygous mutation of the CYP21A2 gene causing 21‑hydroxylase deficiency in a Chinese pedigree.

21-Hydroxylase deficiency (21-OHD) is the most common cause of congenital adrenal hyperplasia. Inherited in an autosomal recessive manner, 21-OHD is caused by mutations in the cytochrome P450 family 21 subfamily A member 2 (CYP21A2) gene. The present study was designed to investigate the genetic characteristics of one Chinese pedigree and to identify the genotype-phenotype association, thereby facilitating the precise diagnosis of 21-OHD at the molecular level. Members of a Chinese family with 21-OHD were screened for mutations in the CYP21A2 gene. Clinical data and biochemical parameters, including androgen and derivatives, were collected. Complete DNA sequencing and multiplex ligation-dependent probe amplification (MLPA) were utilized to analyze the genetic variations in the full-length CYP21A2 gene. A C-T transition located in exon 8 of the CYP21A2 gene, leading to the predicted amino acid residue change from Arg to Trp at codon 342, was identified in the mother and four sisters. Additionally, heterozygous deletion mutations of exons 1, 3, 4, 6 and 7 of paternal origin were detected in the four sisters by MLPA analysis. During the one-year follow-up, the four sisters exhibited symptom improvement following treatment with glucocorticoids, and the proband and one sister successfully conceived. The results of the present study demonstrated that novel compound heterozygous variations in the CYP21A2 gene may be causative agents of 21-OHD, providing insights into the functions of this gene and a more comprehensive understanding of the disorder.

The complete mitochondrial genome of Sanghuangporus sanghuang (Hymenochaetaceae, Basidiomycota)

Sanghuang is a polypore mushroom, which has been widely used in oriental medicine. Since recent molecular phylogenetic studies elucidated its species delimitation, Sanghaungporus sanghuang became the official name of this fungus. In this study, the complete sequence of the mitochondrial DNA of S. sanghuang was determined. The whole genome was 112,060 bp containing 14 proteins, 2 ribosomal RNA subunits, and 45 transfer RNAs. The overall GC content of the genome was 23.21%. A neighbour-joining tree based on atp6 sequence data showed its close relationship with the species of Ganoderma and Trametes.

Complete mitochondrial genome of Pallas’s Leaf Warbler (Phylloscopus proregulus)

In the present study, the complete mitochondrial DNA sequence of Pallas’s Leaf Warbler (Phylloscopus proregulus) was determined for the first time. The mitochondrial genome of Pallas’s Leaf Warbler is a circular molecule of 16,880 bp in size and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions. The base composition is 32.7% for C, 14.3% for G, 30.0% for A and 23.0% for T. These data will be useful for studying the genetic diversity within the species of Pallas’s Leaf Warbler and phylogenetic relationships among different Phylloscopidae species.

The complete chloroplast genome of Artemisia hallaisanensis Nakai (Asteraceae), an endemic medicinal herb in Korea

We determined the complete chloroplast DNA sequence of Artemisia hallaisanensis Nakai, an endemic herbal species distributed on Jeju Island, Korea. The chloroplast DNA is 151,015 bp in length and encodes 4 rRNA, 30 tRNA, and 80 protein-coding genes. Phylogenetic analysis and sequence comparison of protein-coding genes with other Artemisa chloroplast DNAs revealed that the chloroplast genome of A. hallaisanensis is closely related to that of A. capillaris. Additionally, a unique 9 bp deletion in ycf1 gene is specific to A. hallaisanensis.

Does Mitochondrial DNA T2e1 Reflect Traces of Judaism on the “Down-Low”?

The genetic origins of European Jewish women remain controversial and new insights may be obtained through the less studied “other European Jews”, the Sephardim. The branch T2e1 of the mitochondrial DNA phylogenetic tree contains two Sephardic branches distant from one another. To investigate further, the largest analysis of T2e1 to date is presented with 40 new complete T2e1 mitochondrial DNA sequences (mitogenomes) from Europeandescended individuals, doubling the number available. Additionally, nearly 8000 control region sequences from 37 studies were re-considered for T2e1 specifically, from areas high in T2e (Near East, Italy) and areas low in T2e but Sephardic related (Spain, Portugal). These revealed unexpectedly an absence of T2e1 in the Near East and a high number in Spain. By contrast, numerous T2e-Other sequences were in the Near East and Italy with considerable overlap. The mitogenomes elucidated new branches of T2e1 at varying distances from the Sephardic branches including the closest, an Irish-specific clade (4107T), the most populous (nonsynonomous 14180C with unknown biological effect) from Norway (also Sweden, Germany, British Isles), and the root node of T2e1a (2308G) . The findings suggest an origin or early arrival of T2e1 in Europe whilst for T2e, strengthens the role of Near East and its early free travel with the Mediterranean. Quiet Judaism (down-low) may have produced T2e1 branches where Jewish identity was lost, such as from Sephardics who took the Northern route after the Iberian expulsion. The Scandinavian branches may reflect Nordic conquest of British Isles and solve a mystery of a T2e1 hot spot in Iceland. The Near East-Mediterranean origins of T2e resemble that reported for Ashkenazi maternal lineages; other Sephardic haplogroups are needed to assess generality of this common origin. Additional insight may be obtained with the first Jews to enter Europe, the Romaniots, the other other European Jews.

Determination and Analysis of the Complete Mitochondrial DNA Sequence of Octopus dollfusi (Mollusca: Cephalopoda: Octopodidae) from China

Determination and Analysis of the Complete Mitochondrial DNA Sequence of Octopus dollfusi (Mollusca: Cephalopoda: Octopodidae) from China

The complete mitochondrial genome of the Gymnocypris selincuoensis (Cypriniformes: Cyprinidae)

The complete mitochondrial DNA sequence of Gymnocypris selincuoensis was determined and analyzed. This mitochondrial genome was 16,728bp in length and consisted of 37genes in the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis showed that G. selincuoensis is more closely related to G. namensis than to other species.

The diagnostic value and limits of diagnostic parameters for Wilson's disease

Wilson disease (WD) is a rare and treatable genetic disorder. This paper describes the new advances and author's long-term experiences in the diagnosis of WD. The characteristics in clinical and routine tests are: the age of presentation can be quite broad, the WD could not be excluded based on age only; the patients usually have mild digestive symptoms but obvious chronic liver disease signs; liver function tests may reveal normal or a mild elevation in bilirubin, ALT and AST, but quite abnormal in serum albumin and prothrombin time in most patients; Coombs-negative hemolytic anemia, normal or markedly subnormal serum alkaline phosphatase (typically < 40 IU/L) are useful for the diagnosis of fulminant WD. In china, Kayser-Fleischer rings are present in 72.2% of patients at the time of diagnosis, the positive rate is significantly higher in patients with a neurological presentation (93.4%) than patients presenting with liver disease (63.3%), however, they are usually absent in children under 6 years old, occasionly present in patients with chronic cholestatic liver disease. The mean serum ceruloplamin level in WD patients is 71.1 ± 48.7 mg/L, the level is < 200 mg/L in 98.9% of patients, < 100 mg/L in about three fourths patients, < 50 mg/L in about half patients, but it may be low in 50% of patients with severe end-stage liver disease of any etiology too, and even lower than 50 mg/L in patients with nephritic syndrome. Basal 24-hour urinary copper excretion may be≥100 g at presentation in 86.7% of patients with WD, but also in 22% of Patients with certain chronic liver diseases, the sensitivity of penicillamine challenge test is lower than basal urinary copper excretion, however, the specificity is significantly higher than former (97% versus 78%). Hepatic copper determination remains the gold standard for the diagnosis of WD. We have designed a standard method for hepatic copper determination. The most useful cut-off value is 209 g/g dry wt using our method, with the sensitivity of 99.4%, and specificity of 96.1%. However, long-standing hepatic failure and or obstruction can cause heptic copper elevations into the WD area. In recent years, direct complete DNA sequencing has become easy, rapid, less expensive and commercially available. Currently reported mutation detection rate is 90%, the specificity is almost 100%. The limitation to the method has been the ability to identify all the affected alleles in suspected individuals. If no mutation is identified, the diagnosis of WD could not be excluded. None of the laboratory parameters alone allows a definite diagnosis of WD. The WD diagnostic scoring system based on a composite of key parameters helps clinicians to gauge the degree of certainty of the diagnosis: WD scores greater than 4, the diagnosis of WD is highly likely; score 0 or 1, the diagnosis is unlikely. However, the WD diagnosis could not be excluded in suspected patients who do not perform genetic test and hepatic copper determination. Patients with chronic cholestatic liver disease may have scores more than 4.

Comparative Genomic Sequencing and Pathogenic Properties of Equine Herpesvirus 1 KyA and RacL11.

Equine herpesvirus 1 (EHV-1) is a major pathogen affecting equines worldwide. The virus causes respiratory disease, abortion, and, in some cases, neurological disease. EHV-1 Kentucky A (KyA) is attenuated in the mouse and equine, whereas wild-type pathogenic strain RacL11 induces severe inflammatory infiltration of the lung, causing infected mice to succumb. The complete DNA sequencing of the KyA genome revealed that genes UL17 (ORF17), US6 (ORF73; gI), US7 (ORF74; gE), and US8 (ORF75; 10 K) are deleted as compared to the RacL11 and Ab4 genomes. In-frame deletions in the US1 (ORF68), US4 (ORF71; gp2), and UL63 (ORF63; EICP0) genes and point mutations in 14 different open reading frames (ORFs) were detected in the KyA genome. Interestingly, UL1 (ORF1) and UL2 (ORF2) were deleted in both KyA and RacL11. Our previous studies showed that EHV-1 glycoproteins gI, gE, and full-length gp2 contribute to the pathogenesis of the RacL11 strain. The confirmation of these gene deletions in KyA suggests their contribution to the attenuation of this virus. The growth kinetics results revealed that KyA replicates to high titers in cell culture as compared to RacL11 and Ab4, indicating that the above genomic deletions and mutations in KyA do not have an inhibitory effect on KyA replication in cells of mouse, rabbit, equine, or human origin. Studies of EHV-1 pathogenesis in CBA mice showed that KyA is attenuated whereas mice infected with RacL11 succumbed by 3–6 days post-infection, which is consistent with our previous results.

Complete mitochondrial genome of Hemiculter tchangi (Cypriniformes, Cyprinidae)

Hemiculter tchangi, an endemic species to China, is mainly distributed in the upper Yangtze River and its tributaries. In this study, the complete mitochondrial DNA sequence of H. tchangi was first determined by the next-generation sequencing method. The circular mitochondrial genome was 16,621 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 transfer RNAs (tRNA) genes and one non-coding control region (D-loop). As in other teleosts, most mitochondrial genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall nucleotide composition was 30.40% A, 25.40% T, 27.14% C, 17.06% G, with 55.80% AT, respectively. The phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences indicated that H. tchangi showed a close relationship with H. bleekeri bleekeri. The complete mitochondrial genome of H. tchangi would be useful for its identification and conservation.

Complete mitochondrial genome and phylogenetic analysis of Schizothorax molesworthi (Cypriniformes: Cyprinidae)

Schizothorax molesworthi is an endemic species and distributes in the MoTuo reaches of the Yarlung Zangbo River. It is one of the most important commercial fishes in this area. In the present study, the complete mitochondrial DNA sequence of Schizothorax molesworthi was determined and analyzed. The mitochondrial genome of Schizothorax molesworthi is 16,585 bp in length and consisted of 37genes in the typical vertebrate mitochondrial gene arrangement. Overall base composition of mitochondrial genome of Schizothorax molesworthi was 30.1% A, 26.9% C, 17. 4% G, and 25.6% T, with a high A + T content (55.7%). Phylogenetic analysis showed that Schizothorax molesworthi and Schizothorax plagiostomus clustered together in a clade and formed a sister relationship.

Complete mitochondrial genome of the South American fur seal (Arctocephalus australis)

The complete mitochondrial DNA sequence of the South America fur seal (Arctocephalus australis) was obtained by a shotgun sequencing approach. The mitogenome is 16,372 bp in length and includes the genes coding for the two rRNA species (12S and 16S), 13 protein-coding genes, 22 transfer RNA genes, and a control region. The base composition is 33.0% for A, 26.7% for C, 26.1 for T and 14.2% for G, with an overall GC content of 40.9%. The description of this mitogenome will be useful for further phylogeny and genetic studies on Pinnipeds.

The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes.

Passeriformes is the largest group within aves and the phylogenetic relationships between Passeriformes have caused major disagreement in ornithology. Particularly, the phylogenetic relationships between muscicapoidea and sylvioidea are complex, and their taxonomic boundaries have not been clearly defined. Our aim was to study the status of two bird species: Tarsiger cyanurus and Phoenicurus auroreus. Furthermore, we analyzed the phylogenetic relationships of Passeriformes. Complete mitochondrial DNA (mtDNA) sequences of both species were determined and the lengths were 16,803 (T. cyanurus) and 16,772bp (P. auroreus), respectively. Thirteen protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region were identified in these mtDNAs. The contents of A and T at the base compositions was significantly higher than the content of G and C, and this AT skew was positive, while the GC skew was negative. The monophyly of Passeriformes is divided into four major clades: Corvoidea, Sylvioidea, Passeroidea, and Musicicapoidea. Paridae should be separated from the superfamily Sylvioidea and placed within the superfamily Muscicapoidea. The family Muscicapidae and Corvida were paraphyly, while Carduelis and Emberiza were grouped as a sister taxon. The relationships between some species of the order passeriformes may remain difficult to resolve despite an effort to collect additional characters for phylogenetic analysis. Current research of avian phylogeny should focus on adding characters and taxa and use both effectively to obtain a better resolution for deeper and shallow nodes.

Molecular evidence for the occurrence of tomato leaf curl New Delhi virus on chayote (Sechium edule) in southern India.

During 2012-2014, mosaic disease on chayote in the farmers field of Kodaikanal region (high altitude zone) of Tamil Nadu was observed. The disease was characterized with severe mosaic, cupping and enation on leaves with reduced fruit size. Disease was found to causes an yield loss of more than 60% with the maximum disease incidence of 100% for the past 5years consecutively. Preliminary serological and molecular screening indicated the association of begomovirus with the disease. Complete nucleotide sequence and phylogenetic analysis of DNA A revealed the identity of the virus as tomato leaf curl New Delhi virus (ToLCNDV). In recombination analysis study, the major parent was identified as ToLCNDV from Pakistan infecting tomato. Thus the present finding confirms expansion of new geographical region and host for ToLCNDV causing mosaic disease on chayote from Tamil Nadu. To our knowledge this is the first confirmed report for the occurrence of ToLCNDV on chayote in southern India.

The complete mitochondrial genome of the Schizothorax curilabiatus (Cypriniformes: Cyprinidae)

The complete mitochondrial DNA sequence of Schizothorax curilabiatus was determined and analyzed. This mitochondrial genome was 16,578bp in length and showed significant AT bias (55.5% AT content, 44.5% GC content). Phylogenetic analysis showed that S. curilabiatus is more closely related to S. oconnori than to other species. The complete mitochondrial genome sequence provides an important dataset for the exploration of mitochondrial inheritance mechanism.