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Zakea Sultana, Akira Asakura, Sonoko Kinjo, Masafumi Nozawa, Tomoyuki Nakano, Kazuho Ikeo
The hermit crab genus Pagurus exhibits high species diversity and a wide geological distribution. Despite the high species diversity of hermit crabs in the western Pacific coast of Japan, molecular phylogenetic studies of these species have yet to be conducted. To investigate their molecular phylogeny and genetic diversity, we obtained nearly complete mitochondrial genome sequences for ten Pagurus species found along the Pacific coast of Japan by next-generation sequencing, which were compared to other congeners deposited in the GenBank database...
July 10, 2018: Genetica
Linsong Dong, Zhiyong Wang
Genomic prediction is feasible for estimating genomic breeding values because of dense genome-wide markers and credible statistical methods, such as Genomic Best Linear Unbiased Prediction (GBLUP) and various Bayesian methods. Compared with GBLUP, Bayesian methods propose more flexible assumptions for the distributions of SNP effects. However, most Bayesian methods are performed based on Markov chain Monte Carlo (MCMC) algorithms, leading to computational efficiency challenges. Hence, some fast Bayesian approaches, such as fast BayesB (fBayesB), were proposed to speed up the calculation...
June 11, 2018: Genetica
Charlotte Jensen, Michael Ørsted, Torsten Nygaard Kristensen
Habitat fragmentation and small population sizes can lead to inbreeding and loss of genetic variation, which can potentially cause inbreeding depression and decrease the ability of populations to adapt to altered environmental conditions. One solution to these genetic problems is the implementation of genetic rescue, which re-establishes gene flow between separated populations. Similar techniques are being used in animal and plant breeding to produce superior production animals and plants. To optimize fitness benefits in genetic rescue programs and to secure high yielding domestic varieties in animal and plant breeding, knowledge on the genetic relatedness of populations being crossed is imperative...
May 14, 2018: Genetica
Ronny C Woodruff, Michael A Balinski
To increase our understanding of the role of new X-chromosome mutations in adaptive evolution, single-X Drosophila melanogaster males were mated with attached-X chromosome females, allowing the male X chromosome to accumulate mutations over 28 generations. Contrary to our hypothesis that male viability would decrease over time, due to the accumulation and expression of X-linked recessive deleterious mutations in hemizygous males, viability significantly increased. This increase may be attributed to germinal selection and to new X-linked beneficial or compensatory mutations, possibly supporting the faster-X hypothesis...
May 9, 2018: Genetica
Shanshan Gao, Wenfeng Xiong, Luting Wei, Juanjuan Liu, Xing Liu, Jia Xie, Xiaowen Song, Jingxiu Bi, Bin Li
Latrophilin of Tribolium castaneum (Tclph) has been reported to play crucial roles in growth, development and reproduction. However, the regulatory mechanism of Tclph associated with these physiology processes is unknown. Thus, the global transcriptome profiles between RNAi treated (ds-Tclph) and control larvae of T. castaneum were analyzed by RNA-sequencing. Totally, 274 differentially expressed genes (DEGs) were identified between the ds-Tclph and control samples. These DEGs were classified into 42 GO functional groups, including developmental process, reproduction and stress response...
June 2018: Genetica
Niraj Rayamajhi, Jyotsna Sharma
Endemic, obligate outcrossing plant species with narrow geographic distributions and disjunct populations are prone to loss of genetic diversity. Simultaneously, delineating clear species boundaries is important for targeted conservation efforts. The rare and endemic cactus, Sclerocactus brevihamatus subsp. tobuschii (SBT), has a parapatric relationship with Sclerocactus brevihamatus subsp. brevihamatus (SBB) but genetic distance between the two taxa is unknown. We: (1) developed taxon-specific polymorphic microsatellites, (2) assessed genetic diversity within and among nine populations of SBT, and within one population of SBB, and (3) estimated the genetic relationship between the two subspecies...
June 2018: Genetica
Pan Ni, Ali Akbar Bhuiyan, Jian-Hai Chen, Jingjin Li, Cheng Zhang, Shuhong Zhao, Xiaoyong Du, Hua Li, Hui Yu, Xiangdong Liu, Kui Li
Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression...
June 2018: Genetica
Xinkun Hu, Shoufen Dai, Zhongping Song, Dongyang Xu, Zhaojin Wen, Yuming Wei, Dengcai Liu, Youliang Zheng, Zehong Yan
Nine novel high-molecular-weight prolamins (HMW-prolamins) were isolated from Leymus multicaulis and L. chinensis. Based on the structure of the repetitive domains, all nine genes were classified as D-hordeins but not high-molecular-weight glutenin subunits (HMW-GSs) that have been previously isolated in Leymus spp. Four genes, Lmul 1.2, 2.4, 2.7, and Lchi 2.5 were verified by bacterial expression, whereas the other five sequences (1.3 types) were classified as pseudogenes. The four Leymus D-hordein proteins had longer N-termini than those of Hordeum spp...
June 2018: Genetica
Shinpei Yamashita, Tomohiro Takigahira, Kazuo H Takahashi
Accumulating evidence suggests that genotype of host insects influences the development of koinobiont endoparasitoids. Although there are many potential genetic variations that lead to the internal body environmental variations of host insects, association between the host genotype and the parasitoid development has not been examined in a genome-wide manner. In the present study, we used highly inbred whole genome sequenced strains of Drosophila melanogaster to associate single nucleotide polymorphisms (SNPs) of host flies with morphological traits of Asobara japonica, a larval-pupal parasitoid wasp that infected those hosts...
June 2018: Genetica
Vladimir E Gokhman, Valentina G Kuznetsova
Telomeric repeats in two members of the sawfly family Tenthredinidae (Hymenoptera), namely, Tenthredo omissa (Förster, 1844) and Taxonus agrorum (Fallén, 1808) (both have n = 10), were studied using fluorescence in situ hybridization (FISH). Chromosomes of both species were demonstrated to contain the canonical TTAGG insect telomeric repeat, which constitutes the first report of the (TTAGG)n telomeric motif for the Tenthredinidae as well as for the clade Eusymphyta and the suborder Symphyta in general...
June 2018: Genetica
Zhengfei Wang, Yuze Bai, Daizhen Zhang, Boping Tang
Osmoregulation is an important mechanism by which euryhaline crustaceans regulate osmotic and ionic concentrations. The Chinese mitten crab (Eriocheir sinensis) is a strong osmoregulating animal model among crustacean species, as it can maintain its hemolymph composition and survives well in either seawater or freshwater. Osmoregulation by E. sinensis during physiological adaptation has been studied extensively. However, the genetic basis of osmoregulation in E. sinensis for acclimating to changing salinities remains unclear...
June 2018: Genetica
Yoichi Yusa, Natsumi Kumagai
A small number of genes may interact to determine sex, but few such examples have been demonstrated in animals, especially through comprehensive mating experiments. The highly invasive apple snail Pomacea canaliculata is gonochoristic and shows a large variation in brood sex ratio, and the involvement of multiple genes has been suggested for this phenomenon. We conducted mating experiments to determine whether their sex determination involves a few or many genes (i.e., oligogenic or polygenic sex determination, respectively)...
June 2018: Genetica
Yangchun Gao, Shiguo Li, Aibin Zhan
Invasive species cause huge damages to ecology, environment and economy globally. The comprehensive understanding of invasion mechanisms, particularly genetic bases of micro-evolutionary processes responsible for invasion success, is essential for reducing potential damages caused by invasive species. The golden star tunicate, Botryllus schlosseri, has become a model species in invasion biology, mainly owing to its high invasiveness nature and small well-sequenced genome. However, the genome-wide genetic markers have not been well developed in this highly invasive species, thus limiting the comprehensive understanding of genetic mechanisms of invasion success...
April 2018: Genetica
Dan Wang, Lin Zhang, JunFeng Hu, Dianshuai Gao, Xin Liu, Yan Sha
Lipases are physiologically important and ubiquitous enzymes that share a conserved domain and are classified into eight different families based on their amino acid sequences and fundamental biological properties. The Lipase3 family of lipases was reported to possess a canonical fold typical of α/β hydrolases and a typical catalytic triad, suggesting a distinct evolutionary origin for this family. Genes in the Lipase3 family do not have the same functions, but maintain the conserved Lipase3 domain. There have been extensive studies of Lipase3 structures and functions, but little is known about their evolutionary histories...
April 2018: Genetica
Karen M Kiemnec-Tyburczy, Karen E Tracy, Karen R Lips, Kelly R Zamudio
Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker...
April 2018: Genetica
Seo-Jin Lee, Mu-Yeong Lee, Liang-Kong Lin, Y Kirk Lin, Yuchun Li, E-Hyun Shin, Sang-Hoon Han, Mi-Sook Min, Hang Lee, Kyung Seok Kim
Many peninsulas in the temperate zone played an important role as refugia of various flora and fauna, and the southern Korean Peninsula also served as a refugium for many small mammals in East Asia during the Pleistocene. The Asian lesser white-toothed shrew, Crocidura shantungensis, is a widely distributed species in East Asia, and is an appropriate model organism for exploring the role of the Korean Peninsula as a refugium of small mammals. Here, we investigated phylogenetic relationships and genetic diversity based on the entire sequence of the mitochondrial cytochrome b gene (1140 bp)...
April 2018: Genetica
Priscila Rodríguez-Rodríguez, Pedro Luis Pérez de Paz, Pedro A Sosa
Bethencourtia Choisy ex Link is an endemic genus of the Canary Islands and comprises three species. Bethencourtia hermosae and Bethencourtia rupicola are restricted to La Gomera, while Bethencourtia palmensis is present in Tenerife and La Palma. Despite the morphological differences previously found between the species, there are still taxonomic incongruities in the group, with evident consequences for its monitoring and conservation. The objectives of this study were to define the species differentiation, perform population genetic analysis and propose conservation strategies for Bethencourtia...
April 2018: Genetica
Dong-Hui Yan, Qian Gao, Xiaoming Sun, Xiaoyu Song, Hongchang Li
For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s...
April 2018: Genetica
Kurt Langberg, Matthew Phillips, Olav Rueppell
The rate of genomic recombination displays evolutionary plasticity and can even vary in response to environmental factors. The western honey bee (Apis mellifera L.) has an extremely high genomic recombination rate but the mechanistic basis for this genome-wide upregulation is not understood. Based on the hypothesis that meiotic recombination and DNA damage repair share common mechanisms in honey bees as in other organisms, we predicted that oxidative stress leads to an increase in recombination rate in honey bees...
April 2018: Genetica
Ryo Nishijima, Chisa Tanaka, Kentaro Yoshida, Shigeo Takumi
Cuticular wax on the aerial surface of plants has a protective function against many environmental stresses. The bluish-whitish appearance of wheat leaves and stems is called glaucousness. Most modern cultivars of polyploid wheat species exhibit the glaucous phenotype, while in a wild wheat progenitor, Ae. tauschii, both glaucous and non-glaucous accessions exist. Iw2, a wax inhibitor locus on the short arm of chromosome 2D, is the main contributor to this phenotypic variation in Ae. tauschii, and the glaucous/non-glaucous phenotype of Ae...
April 2018: Genetica
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