SciCombinator

Discover the most talked about and latest scientific content & concepts.

Journal: Mitochondrial DNA

26

Abstract Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h = 0.989), while the nucleotide diversity was low (π = 0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST = 0.328, p < 0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved.

Concepts: Mitochondrion, Genetics, Genetic diversity, Channidae, Channa, Biology, DNA, Population genetics

26

Abstract The whale shark Rhincodon typus (Pisces: Chondrichthyes, Orectolobiformes, Rhincodontidae) is the largest living fish on Earth. In this study, we presented its complete mitogenome. It is 16,928 bp in length, contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and one control region with the typical gene order and transcriptional direction in the vertebrates. Overall base composition of the R. typus mitogenome is 33.5% A, 24.3% C, 12.8% G and 29.5% T. Two start codon (GTG and ATG) and two stop codon patterns (TAG and TAA/T) were found in protein-coding genes. The tRNA-Ser2 could not be folded into the typical cloverleaf secondary structure because of the replacement of its dihydrouridine arm by a simple loop. A termination associated sequences (TAS) and three conserved sequence blocks (CSB1-3) were identified in the control region.

Concepts: Gene expression, Georgia Aquarium, Genetic code, RNA, Fish, DNA, Shark, Whale shark

26

Abstract Blue-throated Macaw (Ara glaucogularis) is Critically Endangered species of parrot endemic to small Bolivian area. In this study, full mitochondrial genome of considered species was sequenced. It is 16,983 bp long and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. It`s comparison with published Ara macao mitogenome revealed their high degree of identity. On the other hand, analysis of both the genome compositions showed incompleteness of Ara macao CYTB gene. Hence, mitogenome of Ara macao species occurred only partial sequence. In consequence, Ara glaucogularis mitogenome is the first complete Macaw sequence, which will be indispensable to refine the phylogenetic relationships within the tribe Arini and will enrich the resource of markers for systematic, phylogenetic and population genetic studies.

Concepts: Biology, Blue-throated Macaw, Macaws, Genetics, Ara, DNA, Macaw

26

Abstract Ladybird beetles are generally considered as agriculturally beneficial insects, but the ladybird beetles in the coleopteran subfamily Epilachninae are phytophagous and major plant feeding pest species which causes severe economic losses to cucurbitaceous and solanaceous crops. Henosepilachna pusillanima (Mulsant) is one of the important pest species of ladybird beetle. In this report, we sequenced and characterized the complete mitochondrial genome of H. pusillanima. For sequencing of the complete mitochondrial genome, we used the Ion Torrent sequencing platform. The complete circular mitochondrial genome of the H. pusillanima was determined to be 16,216 bp long. There were totally 13 protein coding genes, 22 transfer RNA, 2 ribosomal RNA and a control (A + T-rich) region estimated to be 1690 bp. The gene arrangement and orientations of assembled mitogenome were identical to the reported predatory ladybird beetle Coccinella septempunctata L. This is the first completely sequenced coleopteran mitochondrial genome from the beetle subfamily Epilachninae from India. Data generated in this study will benefit future comparative genomics studies for understanding the evolutionary relationships between predatory and phytophagous coccinellid beetles.

Concepts: Genetics, Insect, Coccinella septempunctata, DNA, RNA, Beetle, Gene, Coccinellidae

26

Abstract In this work, we report the complete mitochondrial genome sequence of Sus cebifrons (Visayan warty pig). The total length of the mitogenome was 16,475 bp, and its overall base composition was estimated to be 35.0% for A, 25.8% for T, 26.2% for C and 13.0% for G, indicating an A-T (60.8%)-rich feature in Sus cebifrons mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a noncoding control region (D-loop region). The arrangement of these genes was the same as that found in other pigs. The complete mitochondrial genome sequence of the Sus cebifrons would provide new genetic resources for pig domestication study.

Concepts: Bacteria, Suidae, Genetics, Visayan Warty Pig, Pig, Gene, RNA, DNA

26

Abstract Tunisia is located at the crossroads of Europe, the Middle East and Sub-Saharan Africa. This position might lead to numerous waves of migrations, contributing to the current genetic landscape of Tunisians. In this study, we analyzed 815 mitochondrial DNA (mtDNA) sequences from Tunisia in order to characterize the mitochondrial DNA genetic structure of this region, to construct the processes for its composition and to compare it to other Mediterranean populations. To that end, additional 4206 mtDNA sequences were compiled from previous studies performed in African (1237), Near Eastern (231) and European (2738) populations. Both phylogenetic and statistical analyses were performed. This study confirmed the mosaic genetic structure of the Tunisian population with the predominance of the Eurasian lineages, followed by the Sub-Saharan and North African lineages. Among Tunisians, the highest haplogroup and haplotype diversity were observed in particular in the Capital Tunis. No significant differentiation was observed between both geographical (Northern versus Southern Tunisia) and different ethnic groups in Tunisia. Our results highlight the presence of outliers and most frequent unique sequences in Tunisia (10.2%) compared to 45 Mediterranean populations. Phylogenetic analysis showed that the majority of Tunisian localities were closer to North Africans and Near Eastern populations than to Europeans. The exception was found for Berbers from Jerba which are clustered with Sardinians and Valencians.

Concepts: Algeria, Tunis, Sahara, Morocco, Middle East, North Africa, Tunisia, Africa

26

Abstract The northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids have played important roles in the Chinese freshwater aquaculture industry, with an annual production in China exceeding 400 thousand tons. While these are popular aquaculture breeds in China, it is not easy to identify northern snakehead, blotched snakehead, and their hybrids. Thus, a method should be developed to identify these varieties. To distinguish between the reciprocal hybrids (C. argus ♀ × C. maculata ♂ and C. maculata ♀ × C. argus ♂), the mitochondrial genome sequences of northern snakehead and blotched snakehead and their reciprocal hybrids were compared. Following the alignment and analysis of mtDNA sequences of northern snakehead, blotched snakehead and their hybrids, two pairs of specific primers were designed based on identified differences ranging from 12S rRNA to 16S rRNA gene. The BY1 primers amplified the same bands in the blotched snakehead and the hybrid (C. maculata ♀ × C. argus ♂), while producing no products in northern snakehead and the hybrid (C. argus ♀ × C. maculata ♂). Amplification with WY1 yielded the opposite results. Then, 30 individuals per fish were randomized to verify the primers, and the results showed that the primers were specific for breeds, as intended. The specific primers can not only simply distinguish between two kinds of hybrids, but also rapidly identify the two parents. This study provides a method of molecular marker identification to identify reciprocal hybrids.

Concepts: Northern snakehead, Mitochondrial DNA, Channa maculata, Ribosomal RNA, 16S ribosomal RNA, Channidae, DNA, Channa

26

Abstract We have sequenced and characterized the complete mitochondrial DNA of an economically and ecologically important Pacific abalone, Haliotis discus hannai (Haliotidae, Gastropoda). The mitogenome of the Pacific abalone is 16,886 nt total length with a 39.6% G + C composition. Thirty-seven genes were identified including 13 protein-coding, 2 rRNA and 22 tRNA genes. We compared the mitogenome of the Pacific abalone to a putative relative species, H. rubra.

Concepts: Mitochondrial disease, Gene, Gastropoda, Abalone, Mitochondrial DNA, RNA, Mitochondrion, DNA

25

The genus Thymallus has attracted increasing attention in recent years because of its sharp demographic decline. In this study, we reported four complete mitochondrial genomes in the Thymallus genus: Baikal-Lena grayling (T. arcticus baicalolenensis), lower Amur grayling (T. tugarinae), Yalu grayling (T. a. yaluensis), and Mongolian grayling (T. brevirostris). The total length of the four new grayling mtDNAs ranged from 16 658 to 16 663 bp, all of which contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The results suggested that mitochondrial genomes could be a powerful marker for resolving the phylogeny within Thymallinae. Our study validated that the Yalu grayling should be a synonym of the Amur grayling (T. grubii) at the whole mitogenome level. The phylogenetic and dating analyses placed the Amur grayling at the deepest divergence node within Thymallus, diverging at ∼14.95 Ma. The lower Amur grayling diverged at the next deepest node (∼12.14 Ma). This was followed by T. thymallus, which diverged at ∼9.27 Ma. The Mongolian grayling and the ancestor of the sister species, T. arcticus and T. arcticus baicalolenensis, diverged at ∼7.79 Ma, with T. arcticus and T. arcticus baicalolenensis separating at ∼6.64 Ma. Our study provides far better resolution of the phylogenetic relationships and divergence dates of graylings than previous studies.

Concepts: Species, Phylogenetic tree, Biology, Phylogenetics, Organism, Grayling, Thymallus, Salmonidae

25

In this study, we aimed to investigate the associations of mitochondrial DNA (mtDNA) haplogroups and variants with in vitro fertilization (IVF) failure. A retrospective, comparative study of 260 fresh IVF cycles in a Han Chinese population was performed from July 2011 to April 2014. Seventy-three couples had low fertilization rates (≤30%) or total fertilization failure, and 187 controls with normal fertilization were included. Human sperm mtDNA haplogroups and variants were determined by polymerase chain reaction (PCR), nested PCR and direct sequencing. One unreported point variant, A15397G, and two novel deletions at positions 8270-8278 and 8276-8284 were found in this study. A homozygous variant, G9053A in MT-ATP6, was detected in 4 of the 73 cases with fertilization failure, whereas this substitution was not detected in the control group (p < 0.01). The frequency of the point 10397 homozygous variant in MT-ND3 in the IVF failure group was markedly lower than that in the control group (p < 0.05). Furthermore, this study showed that the frequencies of point 8701 and 8943 heterozygous variants in MT-ATP6 in the IVF failure group were also markedly lower than those in the control group (p < 0.05). In addition, the frequency of haplogroup Z was markedly higher in the IVF failure group than in the control group (p < 0.05). Our results suggested that MT-ATP6 variants might be possible causes of IVF failure, but the 10397 homozygous variant in MT-ND3 might help decrease the risk of developing IVF failure. Furthermore, this study indicated that men with haplogroup Z might inherit a higher risk of IVF failure in the Han Chinese population.

Concepts: Haplogroup O3, Population genetics, Mitochondrial Eve, Han Chinese, Polymerase chain reaction, DNA polymerase, In vitro fertilisation, DNA