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https://www.readbyqxmd.com/read/28932936/is-induction-ability-of-seed-germination-of-phelipanche-ramosa-phylogenetically-structured-among-hosts-a-case-study-on-fabaceae-species
#1
Rémi Perronne, Stéphanie Gibot-Leclerc, Fabrice Dessaint, Carole Reibel, Valérie Le Corre
Phelipanche ramosa is a major root-holoparasitic damaging weed characterized by a broad host range, including numerous Fabaceae species. In France, the agricultural threat posed by P. ramosa has increased over two decades due to the appearance of a genetically differentiated pathovar presenting a clear host specificity for oilseed rape. The new pathovar has led to a massive expansion of P. ramosa in oilseed rape fields. The germination rate of P. ramosa seeds is currently known to vary among P. ramosa pathovars and host species...
September 20, 2017: Genetica
https://www.readbyqxmd.com/read/28932924/when-gis-zooms-in-spatio-genetic-maps-of-multipaternity-in-armadillidium-vulgare
#2
Nicolas Bech, Charlotte Depeux, Sylvine Durand, Catherine Debenest, Alexandra Lafitte, Sophie Beltran-Bech
Geographic information system (GIS) tools are designed to illustrate, analyse and integrate geographic or spatial data, usually on a macroscopic scale. By contrast, genetic tools focus on a microscopic scale. Because in reality, landscapes have no predefined scale, our original study aims to develop a new approach, combining both cartographic and genetic approaches to explore microscopic landscapes. For this, we focused on Armadillidium vulgare, a terrestrial isopod model in which evolutionary pressures imposed by terrestrial life have led to the development of internal fertilisation and, consequently, to associated physiological changes...
September 20, 2017: Genetica
https://www.readbyqxmd.com/read/28921302/comparative-evolutionary-genomics-of-corynebacterium-with-special-reference-to-codon-and-amino-acid-usage-diversities
#3
Shilpee Pal, Indrani Sarkar, Ayan Roy, Pradeep K Das Mohapatra, Keshab C Mondal, Arnab Sen
The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium...
September 18, 2017: Genetica
https://www.readbyqxmd.com/read/28916874/development-of-cacta-transposon-derived-scar-markers-and-their-use-in-population-structure-analysis-in-zea-mays
#4
Neha Samir Roy, Kyong-Cheul Park, Sung-Il Lee, Min-Ji Im, Rahul Vasudeo Ramekar, Nam-Soo Kim
Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population...
September 15, 2017: Genetica
https://www.readbyqxmd.com/read/28913775/complete-mitochondrial-genome-of-taharana-fasciana-insecta-hemiptera-cicadellidae-and-comparison-with-other-cicadellidae-insects
#5
Jiajia Wang, Hu Li, Renhuai Dai
Here, we describe the first complete mitochondrial genome (mitogenome) sequence of the leafhopper Taharana fasciana (Coelidiinae). The mitogenome sequence contains 15,161 bp with an A + T content of 77.9%. It includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding (A + T-rich) region; in addition, a repeat region is also present (GenBank accession no. KY886913). These genes/regions are in the same order as in the inferred insect ancestral mitogenome. All protein-coding genes have ATN as the start codon, and TAA or single T as the stop codons, except the gene ND3, which ends with TAG...
September 14, 2017: Genetica
https://www.readbyqxmd.com/read/28905157/landscape-genetics-in-the-subterranean-rodent-ctenomys-chasiquensis-associated-with-highly-disturbed-habitats-from-the-southeastern-pampas-region-argentina
#6
Matías Sebastián Mora, Fernando J Mapelli, Aldana López, María Jimena Gómez Fernández, Patricia M Mirol, Marcelo J Kittlein
Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci...
September 13, 2017: Genetica
https://www.readbyqxmd.com/read/28875394/genomic-based-breeding-tools-for-tropical-maize-improvement
#7
REVIEW
Thammineni Chakradhar, Vemuri Hindu, Palakolanu Sudhakar Reddy
Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions...
September 5, 2017: Genetica
https://www.readbyqxmd.com/read/28831633/characterization-of-major-histocompatibility-complex-class-i-and-class-ii-drb-loci-of-captive-and-wild-indian-leopards-panthera-pardus-fusca
#8
Drashti R Parmar, Siuli Mitra, Snehalata Bhadouriya, Tirupathi Rao, Vaishnavi Kunteepuram, Ajay Gaur
The major histocompatibility complex (MHC), in vertebrate animals, is a multi-genic protein complex that encodes various receptors. During a disease, MHC interacts with the antigen and triggers a cascade of adaptive immune responses to overcome a disease outbreak. The MHC is very important region from immunological point of view, but it is poorly characterized among Indian leopards. During this investigation, we examined genetic diversity for MHC class I (MHC-I) and MHC class II-DRB (MHC-II) among wild and captive Indian leopards...
August 22, 2017: Genetica
https://www.readbyqxmd.com/read/28825201/construction-of-an-integrated-gene-regulatory-network-link-to-stress-related-immune-system-in-cattle
#9
Elham Behdani, Mohammad Reza Bakhtiarizadeh
The immune system is an important biological system that is negatively impacted by stress. This study constructed an integrated regulatory network to enhance our understanding of the regulatory gene network used in the stress-related immune system. Module inference was used to construct modules of co-expressed genes with bovine leukocyte RNA-Seq data. Transcription factors (TFs) were then assigned to these modules using Lemon-Tree algorithms. In addition, the TFs assigned to each module were confirmed using the promoter analysis and protein-protein interactions data...
August 20, 2017: Genetica
https://www.readbyqxmd.com/read/28791584/two-mitochondrial-genomes-in-alcedinidae-ceryle-rudis-halcyon-pileata-and-the-phylogenetic-placement-of-coraciiformes
#10
Xiaomin Sun, Ruoping Zhao, Ting Zhang, Jie Gong, Meidong Jing, Ling Huang
Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region...
August 8, 2017: Genetica
https://www.readbyqxmd.com/read/28776161/diversity-distribution-and-dynamics-of-full-length-copia-and-gypsy-ltr-retroelements-in-solanum-lycopersicum
#11
Rosalía Cristina Paz, Melisa Eliana Kozaczek, Hernán Guillermo Rosli, Natalia Pilar Andino, Maria Virginia Sanchez-Puerta
Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements...
August 3, 2017: Genetica
https://www.readbyqxmd.com/read/28755130/genetic-diversity-and-structure-of-elite-cotton-germplasm-gossypium-hirsutum-l-using-genome-wide-snp-data
#12
XianTao Ai, YaJun Liang, JunDuo Wang, JuYun Zheng, ZhaoLong Gong, JiangPing Guo, XueYuan Li, YanYing Qu
Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0...
July 28, 2017: Genetica
https://www.readbyqxmd.com/read/28730527/characterization-of-the-complete-mitochondrial-genome-of-acanthoscelides-obtectus-coleoptera-chrysomelidae-bruchinae-with-phylogenetic-analysis
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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/28501957/molecular-analysis-reveals-hidden-diversity-in-zungaro-siluriformes-pimelodidade-a-genus-of-giant-south-american-catfish
#19
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...
June 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
#20
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...
June 2017: Genetica
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