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Genetica

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https://www.readbyqxmd.com/read/28730527/characterization-of-the-complete-mitochondrial-genome-of-acanthoscelides-obtectus-coleoptera-chrysomelidae-bruchinae-with-phylogenetic-analysis
#1
Jie Yao, Hong Yang, Renhuai Dai
Acanthoscelides obtectus is a common species of the subfamily Bruchinae and a worldwide-distributed seed-feeding beetle. The complete mitochondrial genome of A. obtectus is 16,130 bp in length with an A + T content of 76.4%. It contains a positive AT skew and a negative GC skew. The mitogenome of A. obtectus contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a non-coding region (D-loop). All PCGs start with an ATN codon, and seven (ND3, ATP6, COIII, ND3, ND4L, ND6, and Cytb) of them terminate with TAA, while the remaining five (COI, COII, ND1, ND4, and ND5) terminate with a single T, ATP8 terminates with TGA...
July 20, 2017: Genetica
https://www.readbyqxmd.com/read/28667419/regulation-of-dna-methylation-on-eef1d-and-rpl8-expression-in-cattle
#2
Xuan Liu, Jie Yang, Qin Zhang, Li Jiang
Dynamic changes to the epigenome play a critical role in a variety of biology processes and complex traits. Many important candidate genes have been identified through our previous genome wide association study (GWAS) on milk production traits in dairy cattle. However, the underlying mechanism of candidate genes have not yet been clearly understood. In this study, we analyzed the methylation variation of the candidate genes, EEF1D and RPL8, which were identified to be strongly associated with milk production traits in dairy cattle in our previous studies, and its effect on protein and mRNA expression...
June 30, 2017: Genetica
https://www.readbyqxmd.com/read/28653298/two-new-miniature-inverted-repeat-transposable-elements-in-the-genome-of-the-clam-donax-trunculus
#3
Eva Šatović, Miroslav Plohl
Repetitive sequences are important components of eukaryotic genomes that drive their evolution. Among them are different types of mobile elements that share the ability to spread throughout the genome and form interspersed repeats. To broaden the generally scarce knowledge on bivalves at the genome level, in the clam Donax trunculus we described two new non-autonomous DNA transposons, miniature inverted-repeat transposable elements (MITEs), named DTC M1 and DTC M2. Like other MITEs, they are characterized by their small size, their A + T richness, and the presence of terminal inverted repeats (TIRs)...
June 26, 2017: Genetica
https://www.readbyqxmd.com/read/28638972/isolation-of-two-new-retrotransposon-sequences-and-development-of-molecular-and-cytological-markers-for-dasypyrum-villosum-l
#4
Jie Zhang, Yun Jiang, Pu Xuan, Yuanlin Guo, Guangbing Deng, Maoqun Yu, Hai Long
Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D...
June 21, 2017: Genetica
https://www.readbyqxmd.com/read/28634866/differential-chromosomal-organization-between-saguinus-midas-and-saguinus-bicolor-with-accumulation-of-differences-the-repetitive-sequence-dna
#5
Dayane Martins Barbosa Serfaty, Natália Dayane Moura Carvalho, Maria Claudia Gross, Marcelo Gordo, Carlos Henrique Schneider
Saguinus is the largest and most complex genus of the subfamily Callitrichinae, with 23 species distributed from the south of Central America to the north of South America with Saguinus midas having the largest geographical distribution while Saguinus bicolor has a very restricted one, affected by the population expansion in the state of Amazonas. Considering the phylogenetic proximity of the two species along with evidence on the existence of hybrids between them, as well as cytogenetic studies on Saguinus describing a conserved karyotypic macrostructure, we carried out a physical mapping of DNA repeated sequences in the mitotic chromosome of both species, since these sequences are less susceptible to evolutionary pressure and possibly perform an important function in speciation...
June 20, 2017: Genetica
https://www.readbyqxmd.com/read/28623426/comparative-physical-mapping-of-18s-rdna-in-the-karyotypes-of-six-leafcutter-ant-species-of-the-genera-atta-and-acromyrmex-formicidae-myrmicinae
#6
Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Hilton Jeferson Alves Cardoso de Aguiar, Silvia das Graças Pompolo
Leafcutter ants of the Atta and Acromyrmex genera are important plagues in different cultures. Cytogenetic data on chromosome number, morphology, and chromosomal banding pattern are only available for 17 species of leafcutter ants. Molecular cytogenetic data for the detection of ribosomal genes by the FISH technique are scarce, and only 15 Neotropical ant species have been studied. This study aimed to physically map the 18S ribosomal RNA genes (rDNA) of six leafcutter ants belonging to the genera Atta and Acromyrmex using FISH...
June 16, 2017: Genetica
https://www.readbyqxmd.com/read/28567603/nearly-complete-mitogenome-of-hairy-sawfly-corynis-lateralis-brull%C3%A3-1832-hymenoptera-cimbicidae-rearrangements-in-the-iqm-and-arns1ef-gene-clusters
#7
Özgül Doğan, E Mahir Korkmaz
The Cimbicidae is a small family of the primitive and relatively less diverse suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genome (mitogenome) of hairy sawfly, Corynis lateralis (Hymenoptera: Cimbicidae) was sequenced using next generation sequencing and comparatively analysed with the mitogenome of Trichiosoma anthracinum. The sequenced length of C. lateralis mitogenome was 14,899 bp with an A+T content of 80.60%. All protein coding genes (PCGs) are initiated by ATN codons and all are terminated with TAR or T- stop codon...
May 31, 2017: Genetica
https://www.readbyqxmd.com/read/28501957/molecular-analysis-reveals-hidden-diversity-in-zungaro-siluriformes-pimelodidade-a-genus-of-giant-south-american-catfish
#8
Antonio A Pires, Jorge L Ramirez, Pedro M Galetti, Waldo P Troy, Patricia D Freitas
The genus Zungaro contains some of the largest catfish in South America. Two valid species are currently recognized: Zungaro jahu, inhabiting the Paraná and Paraguay basins, and Zungaro zungaro, occurring in the Amazonas and Orinoco basins. Analysing Zungaro specimens from the Amazonas, Orinoco, Paraguay and Paraná basins, based on the sequencing of COI and D-loop, we found at least three MOTUs, indicating the existence of hidden diversity within this fish group. Considering the ecological and economic values of this fish, our results are surely welcomed for its conservation, disclosing new findings on its diversity and pointing out the necessity for a detailed taxonomic revision...
May 13, 2017: Genetica
https://www.readbyqxmd.com/read/28439758/molecular-phylogeny-of-21-tropical-bamboo-species-reconstructed-by-integrating-non-coding-internal-transcribed-spacer-its1-and-2-sequences-and-their-consensus-secondary-structure
#9
Jayadri Sekhar Ghosh, Samik Bhattacharya, Amita Pal
The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses...
April 24, 2017: Genetica
https://www.readbyqxmd.com/read/28429244/fluctuating-asymmetry-of-meristic-traits-an-isofemale-line-analysis-in-an-invasive-drosophilid-zaprionus-indianus
#10
Lilian Madi-Ravazzi, Luis Fernando Segala, Vincent Debat, Jean R David
Metric (e.g., body size) and meristic (e.g., bristle number) traits are of general use in quantitative genetic studies, and the phenotypic variance is subdivided into a genetic and a non-genetic environmental component. The non-genetic variance may have two origins: a common garden effect between individuals and a developmental instability within the same individual. Developmental instability may be studied by considering the fluctuating asymmetry (FA) between the two sides of the body. The isofemale line technique is a convenient method for investigating the architecture of natural populations but has been rarely implemented for investigating FA...
April 20, 2017: Genetica
https://www.readbyqxmd.com/read/28424974/transposable-elements-in-the-anopheles-funestus-transcriptome
#11
Rita D Fernández-Medina, Claudia M A Carareto, Cláudio J Struchiner, José M C Ribeiro
Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized...
April 19, 2017: Genetica
https://www.readbyqxmd.com/read/28421323/gene-expression-nucleotide-composition-and-codon-usage-bias-of-genes-associated-with-human-y-chromosome
#12
Monisha Nath Choudhury, Arif Uddin, Supriyo Chakraborty
Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position...
April 18, 2017: Genetica
https://www.readbyqxmd.com/read/28389974/lmi1-like-genes-involved-in-leaf-margin-development-of-brassica-napus
#13
Xiyuan Ni, Han Liu, Jixiang Huang, Jianyi Zhao
In rapeseed (Brassica napus L.), leaf margins are variable and can be entire, serrate, or lobed. In our previous study, the lobed-leaf gene (LOBED-LEAF 1, BnLL1) was mapped to a 32.1 kb section of B. napus A10. Two LMI1-like genes, BnaA10g26320D and BnaA10g26330D, were considered the potential genes that controlled the lobed-leaf trait in rapeseed. In the present study, these two genes and another homologous gene (BnaC04g00850D) were transformed into Arabidopsis thaliana (L.) Heynh. plants to identify their functions...
April 7, 2017: Genetica
https://www.readbyqxmd.com/read/28271308/genetic-structure-of-a-regionally-endangered-orchid-the-dark-red-helleborine-epipactis-atrorubens-at-the-edge-of-its-distribution
#14
Hilde Hens, Anne Jäkäläniemi, Kadri Tali, Petr Efimov, Alexey V Kravchenko, Laura Kvist
The genetic structure and diversity of species is determined by both current population dynamics and historical processes. Population genetic structure at the edge of the distribution is often expected to differ substantially from populations at the centre, as these edge populations are often small and fragmented. In addition, populations located in regions that have experienced repeated glaciations throughout the Pleistocene, may still carry imprints from the genetic consequences of frequent distribution shifts...
April 2017: Genetica
https://www.readbyqxmd.com/read/28271307/the-role-of-ecological-factors-in-determining-phylogeographic-and-population-genetic-structure-of-two-sympatric-island-skinks-plestiodon-kishinouyei-and-p-stimpsonii
#15
Kazuki Kurita, Mamoru Toda
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history...
April 2017: Genetica
https://www.readbyqxmd.com/read/28243829/meiotic-pairing-as-an-indicator-of-genome-composition-in-polyploid-prairie-cordgrass-spartina-pectinata-link
#16
Jeffrey W Bishop, Sumin Kim, María B Villamil, D K Lee, A Lane Rayburn
The existence of neopolyploidy in prairie cordgrass (Spartina pectinata Link) has been documented. The neohexaploid was discovered coexisting with tetraploids in central Illinois, and has been reported to exhibit competitiveness in the natural environment. It is hypothesized that the natural tetraploid cytotype produced the hexaploid cytotype via production of unreduced gametes. Meiosis I chromosome pairing was observed in tetraploid (2n = 4x = 40), hexaploid (2n = 6x = 60), and octoploid (2n = 8x = 80) accessions and the percentage of meiotic abnormality was determined...
April 2017: Genetica
https://www.readbyqxmd.com/read/28238053/a-possible-genetic-basis-for-vulnerability-in-euphydryas-maturna-lepidoptera-nymphalidae
#17
Katalin Pecsenye, Andrea Tóth, Judit Bereczki, Zoltán Varga
Nearly all of the known populations of Scarce Fritillary, Euphydryas maturna (Linnaeus, 1758), are declining in Western and Central Europe. In order to identify the possible reasons for its vulnerability we surveyed the population genetics of this butterfly species using multi-locus genotype data. Females of our target species lay lots of eggs in one or two batches only and pre-hibernation caterpillars live and feed gregariously in a nest. As a consequence, a random unfavourable event can eliminate most offspring of a particular female resulting in a strong genetic drift effect combined with inbreeding...
April 2017: Genetica
https://www.readbyqxmd.com/read/28238052/estimation-of-loci-involved-in-non-shattering-of-seeds-in-early-rice-domestication
#18
Ryo Ishikawa, Akinori Nishimura, Than Myint Htun, Ryo Nishioka, Yumi Oka, Yuki Tsujimura, Chizuru Inoue, Takashige Ishii
Rice (Oryza sativa L.) is widely cultivated around the world and is known to be domesticated from its wild form, O. rufipogon. A loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. Previously, three seed-shattering loci, qSH1, sh4, and qSH3 were reported to be involved in non-shattering of seeds of Japonica-type cultivated rice, O. sativa cv. Nipponbare. In this study, we focused on non-shattering characteristics of O. sativa Indica cv. IR36 having functional allele at qSH1...
April 2017: Genetica
https://www.readbyqxmd.com/read/28233217/genetic-diversity-and-structure-of-the-zombi-pea-vigna-vexillata-l-a-rich-gene-pool-based-on-ssr-marker-analysis
#19
Sujinna Dachapak, Prakit Somta, Supalak Poonchaivilaisak, Tarika Yimram, Peerasak Srinives
Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure...
April 2017: Genetica
https://www.readbyqxmd.com/read/28204905/transcriptome-assembly-and-identification-of-genes-and-snps-associated-with-growth-traits-in-largemouth-bass-micropterus-salmoides
#20
Shengjie Li, Hao Liu, Junjie Bai, Xinping Zhu
Growth is one of the most crucial economic traits of all aquaculture species, but the molecular mechanisms involved in growth of largemouth bass (Micropterus salmoides) are poorly understood. The objective of this study was to screen growth-related genes of M. salmoides by RNA sequencing and identify growth-related single-nucleotide polymorphism (SNP) markers through a growth association study. The muscle transcriptomes of fast- and slow-growing largemouth bass were obtained using the RNA-Seq technique. A total of 54,058,178 and 54,742,444 qualified Illumina read pairs were obtained for the fast-growing and slow-growing groups, respectively, giving rise to 4,865,236,020 and 4,926,819,960 total clean bases, respectively...
April 2017: Genetica
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