Genetic structure of Salsola junatovii (Chenopodiaceae) in the northern edge of the Taklimakan desert and conservational implications
Publication date: August 2016 Source:Biochemical Systematics and Ecology, Volume 67 Author(s): Zhibin Wen, Zhe Xu, Xiaojun Shi, Jie Zhang, Mingli Zhang Salsola junatovii Botsch. (Chenopodiaceae), a desert shrub endemic to the northern edge of the Taklimakan desert in China, is listed as an endangered species because of its narrow habitat requirements and a decline in numbers of individuals. In order to provide information on conservation strategies, we investigated the genetic patterns and evolutionary history of this species. Two cpDNA spacers, (psbA-trnH and psbK-psbI), and the nrITS sequence were employed in 116 ...
Source: Biochemical Systematics and Ecology - June 7, 2016 Category: Biochemistry Source Type: research

Molecular diversity and phylogeography of Andricus curtisii (Hymenoptera, Cynipidae) in Turkey
Publication date: August 2016 Source:Biochemical Systematics and Ecology, Volume 67 Author(s): Serap Mutun A 433-bp fragment of the mitochondrial cytochrome b gene and the entire nuclear ITS2 region were sequenced in an oak gall wasp species, Andricus curtisii, which represents 21 populations across its range in Turkey. Forty cytochrome b haplotypes and 63 ITS2 alleles were discovered among the 161 individuals studied. Remarkable genetic variation was detected in the species, with an average haplotype diversity (h) of 0.72 and 0.76 and an average nucleotide diversity (π) of 0.06 and 0.01 for the cyt b gene and the IT...
Source: Biochemical Systematics and Ecology - June 5, 2016 Category: Biochemistry Source Type: research

Cytoplasmic diversity, phylogenetic relationships and molecular evolution of Tunisian Citrus species as inferred from mutational events and pseudogene of chloroplast trnL-trnF spacer
In this report, cytoplasmic polymorphism of twenty seven Tunisian Citrus cultivars was explored using the chloroplast trnL-trnF intergenic spacer. Chloroplast sequences showed variation in length and nucleotide content. Haplotype and nucleotide diversity showed low variations. Molecular phylogenetic tree identifies Citrus maternal origins and demonstrates two major groups distinguishing between mandarin and pummelo groups. The trnL-trnF intergenic spacer showed one copy of pseudogene of the original trnF gene in 27 Citrus species at position 275 bp with a size varying from 49 to 63 bp. The anticodon domain was id...
Source: Biochemical Systematics and Ecology - June 3, 2016 Category: Biochemistry Source Type: research

Spreading of the Chinese pond mussel, Sinanodonta woodiana, across Wallacea: One or more lineages invade tropical islands and Europe
Publication date: August 2016 Source:Biochemical Systematics and Ecology, Volume 67 Author(s): Ivan N. Bolotov, Yulia V. Bespalaya, Mikhail Y. Gofarov, Alexander V. Kondakov, Ekaterina S. Konopleva, Ilya V. Vikhrev Here we report the first molecular data on an invasive Sinanodonta woodiana (Lea, 1834) (Bivalvia: Unionidae) population from Lesser Sundas (Flores Island, Indonesia). The DNA barcoding reveals that this population belongs to a mitochondrial lineage that is widely distributed across Malaysia. The mean COI p-distance between this ‘tropical’ lineage and invasive European populations is 5.3 ...
Source: Biochemical Systematics and Ecology - June 3, 2016 Category: Biochemistry Source Type: research

Phenolic constituents of leaves from Persea caerulea Ruiz & Pav; Mez (Lauraceae)
Publication date: August 2016 Source:Biochemical Systematics and Ecology, Volume 67 Author(s): Juan M. Alvárez, Luis E. Cuca, Alegría Carrasco-Pancorbo, Ana Belén Ruiz-Muelle, Ignacio Fernández, Alberto Fernández-Gutiérrez The chemical investigation of the ethanolic extract from the leaves of Persea caerulea led to the isolation of flavonoids, coumarins and three steroidal type compounds. Based on ESI-MS, UV, IR, GC-MS and 1H and 13C NMR data analysis, the structures of ten isolated compounds were identified as: quercetin (1), kaempferide-3-O-α-l-rhamnopyranoside (2),...
Source: Biochemical Systematics and Ecology - June 3, 2016 Category: Biochemistry Source Type: research

Complete mitochondrial genomes of three sea basses Lateolabrax (Perciformes, Lateolabracidae) species: Genome description and phylogenetic considerations
Publication date: August 2016 Source:Biochemical Systematics and Ecology, Volume 67 Author(s): Binbin Shan, Na Song, Zhiqiang Han, Jun Wang, Tianxiang Gao, Koji Yokogawa Genus Lateolabrax consists of three species, Japanese sea bass Lateolabrax japonicus, spotted sea bass Lateolabrax maculatus and blackfin sea bass Lateolabrax latus. The complete mitochondrial DNA (mtDNA) of the three sea basses were amplified and sequenced to characterize and discuss their phylogenetic relationships. The length of mitogenomes was 16,593 bp, 16,479 bp and 16,600 bp, respectively, and all of them consisted of 13 prote...
Source: Biochemical Systematics and Ecology - May 31, 2016 Category: Biochemistry Source Type: research

Molecular polymorphism of MHC-DRB gene and genetic diversity analysis of captive forest musk deer (Moschus berezovskii)
In this study, we investigated the MHC variation in 51 forest musk deer (Moschus berezovskii) collected from three captive populations in Sichuan Province, China. Seventeen haplotypes were isolated from the 51 samples. A total of 51 mutation sites were identified and yielded a nucleotide diversity of 0.056. These haplotype sequences possessed 83 putative amino acid sites, including 24 PBR sites (peptide binding region) and 59 non-PBR sites. Out of 24 PBR sites, 15 codons showed variation (0.625), while 12 codons showed variation (0.203) in 59 non-PBR sites. Non-synonymous substitutions primarily occurred in PBR, with analy...
Source: Biochemical Systematics and Ecology - May 31, 2016 Category: Biochemistry Source Type: research

Detection of rare and invasive freshwater fish species using eDNA pyrosequencing: Lake Iznik ichthyofauna revised
This study is the first environmental DNA study designed to assess complete ichthyofauna of the largest lake in Marmara Region of Turkey. For this purpose, an eDNA metabarcoding approach enhanced with tagged primers according to sampling stations for a station specific species listing was used to revise the ichthyofauna of Lake Iznik. Results of pyrosequencing data indicate the presence of 23 species in the lake, five of which are reported for the first time. Short fragment of cytochrome b gene sequences amplified in this study were able to make identifications at species level and the eDNA metabarcoding approach was more ...
Source: Biochemical Systematics and Ecology - May 31, 2016 Category: Biochemistry Source Type: research

Genetic diversity and population structure of Capitulum mitella (Cirripedia: Pedunculata) in China inferred from mitochondrial DNA sequences
In this study, the phylogeographical pattern, population genetic profile, and demographic history of C. mitella were investigated using mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI). A 599-bp segment of this subunit was sequenced from 198 individuals sampled in eight localities along the Chinese coast. High haplotype diversity (0.656–0.788) and low nucleotide diversity (0.0016–0.00244) were observed. Analyses of molecular variance (AMOVA) and F ST statistics suggested the absence of a significant population structure. Neutrality tests and mismatch distributions both indicated a recent populatio...
Source: Biochemical Systematics and Ecology - May 31, 2016 Category: Biochemistry Source Type: research

A new flavone glycoside from the leaves of Agastache rugosa (Fisch. & C.A.Mey.) Kuntze
In this study, one new flavone glycoside (1) along with six flavonoids (2–7), nine phenyl glycosides (8–16) and three megastigmane glycosides (17–19) were isolated from the leaves of A. rugosa. By extensive spectroscopic methods including 1D and 2D NMR, and MS data, the structure of the new compound (1) was elucidated as acacetin 7-O-β-(6″-(E)-crotonylglucopyranoside). From present investigation, compound 1 and 7–19 were isolated for the first time from the genus Agastache and 1, 16, 18 and 19 in the Lamiaceae family. Graphical abstract (Source: Biochemical Systematics and Ecology)
Source: Biochemical Systematics and Ecology - May 31, 2016 Category: Biochemistry Source Type: research

Insights into biosynthetic genes involved in the secondary metabolism of Gardenia jasminoides Ellis using transcriptome sequencing
Publication date: August 2016 Source:Biochemical Systematics and Ecology, Volume 67 Author(s): Chun-xia Yang, Ting Zhang, Meng Xu, Pei-lin Zhu, Shao-yong Deng Gardenia jasminoides is an economically important woody plant in Asia. It contains multiple secondary metabolites in its fruit that are used in Chinese traditional medicines for treating diseases and as a natural colorant for food. However, little is known at the genetic level about how secondary metabolites are biosynthesized in this plant. Thus, transcriptome sequencing of G. jasminoides fruit at two developmental stages was performed using the Illumina sequ...
Source: Biochemical Systematics and Ecology - May 31, 2016 Category: Biochemistry Source Type: research

Triterpene saponins from Fagonia scabra Forssk and other Fagonia species
This article reports on the structure of triterpenoids saponins (1–49) isolated from Fagonia species. In addition, it describes one known flavonoid (50) with luteolin as aglycone and seven known triterpenoid saponins (26, 51–56) isolated from the aerial parts of Fagonia scabra Forssk. Compounds 50–56, were isolated for the first time from the genus Fagonia, while compounds 50–53, 55–56 have never been encountered in the Zygophyllaceae family. The chemotaxonomic relationship between F. scabra and other Fagonia species was also discussed. (Source: Biochemical Systematics and Ecology)
Source: Biochemical Systematics and Ecology - May 30, 2016 Category: Biochemistry Source Type: research

Caraway essential oil composition and morphology: The role of location and genotype
In this study, wild populations and commercial cultivars from the Nordic germplasm collection were examined. Plants were grown in two locations (Iceland and Sweden) and essential oil composition and phenotypic characteristics identified. Carvone and limonene were the two major compounds detected at levels around 14 and 70% of total peak area, respectively. Also p-cymene, trans-β-ocimene, α-Terpinolene and myrcene each were detected at levels above or around 2%. In total, 47 compounds were detected of which 40 were identified. The effects of material type and location were established, where location had a greate...
Source: Biochemical Systematics and Ecology - May 28, 2016 Category: Biochemistry Source Type: research

Development of novel microsatellite loci and analyses of genetic diversity in the endangered Tanakia somjinensis
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Hyung-Bae Jeon, Junghwa An, Seon-Man Kweon, Soonok Kim, Jeong-Nam Yu, Byung-Jik Kim, Seigo Kawase, Ho Young Suk Somjin bitterling (Tanakia somjinensis), an endemic cyprinid on the Korean Peninsula, is critically endangered with only a few small populations found in limited areas in a single drainage, raising concerns that this species has likely suffered low levels of genetic variability. In the current study, 23 polymorphic microsatellite markers were developed using Illumina paired-end sequencing for quantification of t...
Source: Biochemical Systematics and Ecology - May 26, 2016 Category: Biochemistry Source Type: research

Genetic diversity of orchardgrass (Dactylis glomerata L.) cultivars revealed by simple sequence repeats (SSR) markers
In this study, the SSR molecular markers were used to characterize the genetic diversity in 19 specimens of orchardgrass cultivars collected from China and other countries. Two hundred and nine amplified bands from 25 SSR primer pairs were selected for genetic analysis, among which 192 bands (91.5%) were found to be polymorphic. The polymorphism information content ranges between 0.17 and 0.44, the genetic similarity coefficient ranges between 0.7134 and 0.8672, and the genetic distance ranges between 0.1425 and 0.3377. The data showed that SSR molecular markers can detect more genetic loci, and could be taken as an effect...
Source: Biochemical Systematics and Ecology - May 26, 2016 Category: Biochemistry Source Type: research

Population genetic structure and identification of loci under selection in the invasive tunicate, Botryllus schlosseri, using newly developed EST-SSRs
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Yaping Lin, Aibin Zhan Botryllus schlosseri, also known as golden star tunicate, is generally considered of European origin and has successfully invaded coastal waters of all continents except Antarctica. Owing to its significantly negative ecological impacts, it is crucial to understand its dispersal dynamics and mechanisms of invasion success. Here, we identified 1020 microsatellite-containing sequences from 98,626 expressed sequence tags (ESTs), and developed and characterized 17 polymorphic microsatellites (i.e. EST-SSRs) b...
Source: Biochemical Systematics and Ecology - May 26, 2016 Category: Biochemistry Source Type: research

Development and characterization of 26 polymorphic microsatellite markers in Lateolabrax maculatus and cross-species amplification for the phylogenetically related taxa
In this study, we developed 26 polynucleotide-repeat microsatellite loci for L. maculatus through high-throughput DNA sequencing technology. The number of alleles per locus ranged from 3 to 19. Observed and expected heterozygosities varied from 0.188 to 0.906 and 0.175 to 0.938, respectively. One locus showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni correction. These 26 novel microsatellite markers will serve as useful tools which benefit population genetics studies and conservation management of L. maculatus. In addition, cross-species amplification tests showed that the transferability of 6 ...
Source: Biochemical Systematics and Ecology - May 26, 2016 Category: Biochemistry Source Type: research

Genetic diversity and population structure of endangered endemic Paeonia jishanensis in China and conservation implications
This study carries significant implications for the conservation and utilization of this endangered species. (Source: Biochemical Systematics and Ecology)
Source: Biochemical Systematics and Ecology - May 22, 2016 Category: Biochemistry Source Type: research

Ecology-types determine physicochemical properties and microbial communities of sediments obtained along the Songhua River
This study suggests that sites of similar ecology-types affect the microbial communities in a similar manner, and result in increased heterogeneity in ecological landscapes. (Source: Biochemical Systematics and Ecology)
Source: Biochemical Systematics and Ecology - May 20, 2016 Category: Biochemistry Source Type: research

Spatial genetic structure in natural populations of the overexploited tree Eremanthus erythropappus (DC.) macleish (Asteraceae)
This study uses spatial statistical analyses to assess the SGS in nine locations with diverse landscape characteristics where Eremanthus erythropappus occurs at varying densities. This species, commonly known as candeia, is widely distributed throughout Minas Gerais State, Brazil, and its wood has high economic value due to its natural durability and production of oil containing the active ingredient alpha-bisabolol. The species has undergone intense exploitation without adequate management planning. Our analyses were based on polymorphism at nine inter-simple sequence repeat (ISSR) loci. We observed SGS in five of the nin...
Source: Biochemical Systematics and Ecology - May 20, 2016 Category: Biochemistry Source Type: research

“Gone with the wind”: Fatty acid biomarkers and chemotaxonomy of stranded pleustonic hydrozoans (Velella velella and Physalia physalis)
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Ana Rita Lopes, Miguel Baptista, Inês C. Rosa, Gisela Dionísio, José Gomes-Pereira, José Ricardo Paula, Cátia Figueiredo, Narcisa Bandarra, Ricardo Calado, Rui Rosa Marine pleustonic species such as the hydrozoans Velella velella and Physalia physalis, are known to drift in the world's oceans driven by winds, currents and tides. Here we present the first chemotaxonomic characterization, based on the fatty acid (FA) profile, of these two charismatic oceanic species that thrive in the int...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Chemical constituents from Lespedeza cuneata G. Don (Leguminosae)
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Jin Young Min, Sang Hee Shim Phytochemical investigation of Lespedeza cuneata led to the isolation of seventeen compounds including three steroids (β-sitosterol 1, β-sitosterol-6′-linolenoyl-3-O-β-d-glucopyranoside 3, and β-sitosterol glucoside 13), nine flavonoids (quercetin 4, kaempferol 5, isovitexin 8, hirsutrin 9, nicotiflorin 10, vitexin 11, astragalin 12, trifolin 14, and isorhamnetin 17), two phenolics (benzyl-β-d-glucopyranoside 7 and homovanillyl alcohol 16), one carotenoid (loroxanthin ...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Genetic diversity and population structure of the endangered medicinal plant Phellodendron amurense in China revealed by SSR markers
In this study, eight nuclear SSR primer pairs were employed to assess the genetic diversity and structure of 22 natural populations, including 516 individuals. A total of 66 alleles were detected with an average of 8.3 alleles per locus ranging from 3 to 17. The expected heterozygosity (He) of each SSR locus varied from 0.347 to 0.877 (average 0.627). Analysis of molecular variance (AMOVA) revealed that the main variation component existed within populations (95.11%) rather than among populations (4.89%). The Wilcoxon's sign-rank tests did not show any recent bottleneck effect in any population. A Mantel test displayed a s...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Identification of Odontamblyopus lacepedii via morphology and DNA barcoding
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Zisha Liu, Na Song, Takashi Yanagimoto, Zhuocheng Zhou, Jinquan Yang, Tianxiang Gao To evaluate taxonomic and genetic variation in Odontamblyopus lacepedii collected in East Asia, morphometric characters and molecular analysis were described. The body was ribbon-like. The body and head were grayish-purple with no embedded scales. Eyes were rudimentary, but distinct, covered by skin. The dorsal and anal fins were continuous with the caudal fin. The edges of the dorsal, anal, and caudal fins were dark chocolate-brown. Genetic...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Genetic diversity of Ulmus lamellosa by morphological traits and sequence-related amplified polymorphism (SRAP) markers
In this study, the genetic diversity of 16 natural populations of U. lamellosa was evaluated by morphological traits and sequence-related amplified polymorphism (SRAP) markers. The morphological data showed that significant difference was found among 14 morphological traits. Coefficient of variation (CV) and phenotypic differentiation coefficient (V ST) were 27.2% and 27.3% respectively. Based on SRAP markers, the percentage of polymorphic bands (PPB) of U. lamellosa populations was 82.7%. Nei's gene diversity (He) and Shannon's information index (I) were 0.22 and 0.36 respectively. High genetic differentiation was detecte...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Genetic structure and diversity of Glehnia littoralis, an endangered medicinal plant in China
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Ailan Wang, Ping Zhang, Xiao Liu, Jianguang Liang, Weiwei Li The medicinal plant Glehnia littoralis has become increasingly endangered in China. To assist in the formulation of conservation strategies for this species, we assessed the genetic diversity of G. littoralis with a total of 172 samples from 10 populations using SRAP markers. The results showed that Nei's gene diversity (H) per locus ranged from 0.04 to 0.2504, with an average of 0.245, and that Shannon's information index (I) ranged from 0.233 to 0.6253, averaging...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

The complete mitochondrial genome of Triplophysa lixianensis (Teleostei: Cypriniformes: Balitoridae) with phylogenetic consideration
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Huifang Jing, Pengfei Yan, Wei Li, Xiaoyan Li, Zhaobin Song The complete mitochondrial genome of Triplophysa lixianensis was 16,570 bp in size and consisted of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes as well as a control region. The gene arrangement, nucleotide composition, and the codon usage pattern of the mitochondrial genome of T. lixianensis were similar to those of other kinds of teleosts. Nucleotide composition of the whole mitogenome was 27.81% A, 28.45% T, 25.36% C,...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Complete mitochondrial genome and phylogeny of Microhyla butleri (Amphibia: Anura: Microhylidae)
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Hoi-Sen Yong, Sze-Looi Song, Phaik-Eem Lim, Praphathip Eamsobhana, Ji Tan The whole mitochondrial genome of Microhyla butleri was determined by next-generation sequencing of mitochondrial DNA. It had a total length of 16,720 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions (L-strand replication origin and control region). The control region (1338 bp) was flanked by cob and trnL1 genes. The start codons included 11 ATG, 1 ATA and 1 GTG. Three PCGs had TAA, 3 had AGG, 1 ...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Development and characterization of 29 microsatellite markers for Ligumia nasuta (Bivalvia: Unionidae) using an Illumina sequencing approach
This study used Illumina paired-end shotgun sequencing to identify potential microsatellite loci for L. nasuta, utilizing two samples to develop the Illumina paired-end shotgun library. Forty-eight primer pairs were tested on the remaining 24 samples. Twenty-nine of the 48 microsatellite primer sets screened were successfully amplified using 24 L. nasuta samples collected from the Great Lakes watershed. The estimated fragment size ranged from 167 to 445 base-pairs (bp) and the number of alleles per locus varied between 5 and 16 (mean = 9.7). Only five of the loci deviated significantly from Hardy–Weinberg e...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Phylogenetic analyses and evolutionary timescale of Coleoptera based on mitochondrial sequence
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Hongli Zhang, Nian Liu, Zhiping Han, Jianxia Liu Coleopteran phylogeny was analysed using mitochondrial genome (mitogenome) sequence. The optimal tree topology was given by the dataset consisted of all coding genes except for the exclusion of the 3rd codon sites (mtDNA12) using Bayesian Inference Method. This topology supports the monophyly of four suborders, and the sister group relationship between Adephaga and Myxophaga and between Polyphaga and Archostemata. In Polyphaga, Cucujiformia and Elateroidea formed independent no...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Microsatellite markers for barnacle studies: Isolation and characterization of polymorphic microsatellite loci from the invasive barnacle Megabalanus coccopoma (Darwin, 1854) and its cross-amplification in the Southern Atlantic endemic species Megabalanus vesiculosus (Darwin, 1854)
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Nívia Maria Nunes Abreu, Isabela Marçal, Angela Borges Duarte, Fabio Bettini Pitombo, Anderson Vilasboa, Jaqueline Gusmão Megabalanus coccopoma (Darwin, 1854), an important invasive species in the world scenario, is included in one of the most common barnacle genus known. Nine new polymorphic microsatellite loci from M. coccopoma and cross-amplification tests of these primers in the Brazilian endemic species Megabalanus vesiculosus (Darwin, 1854) are described. Allele numbers varied between seven and 21...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Genetic diversity and differentiation of the Critically Endangered Hispaniolan palm Coccothrinax jimenezii M.M. Mejía & R.G. García based on novel SSR markers
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Brett Jestrow, Brígido Peguero, Francisco Jiménez, William Cinea, Michael Hass, Andrew Reeve, Alan W. Meerow, M. Patrick Griffith, Michael Maunder, Javier Francisco-Ortega Coccothrinax jimenezii M.M. Mejía & R.G. García is a Critically Endangered palm species restricted to Haiti (one population near the city of Gonaïves with 43 individuals) and the Dominican Republic (one population on the shores of Lago Enriquillo with 18 individuals). The species faces two major conservation ch...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Identification of candidate AFLP markers for shell color of the Pacific oyster (Crassostrea gigas) under artificial selection
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Junlin Song, Qi Li, Lingfeng Kong, Hong Yu The shell color of the Pacific oyster (Crassostrea gigas) is a desirable trait, but only a few genetic studies on shell color have been documented. Through successive selective breeding, four shell color variants of white (W), gold (G), black (B) and purple (P) C. gigas have been developed. The amplified fragment length polymorphism (AFLP) technique was used to scan the genomes of the four variants with different shell colors and one wild population (C) to identify candidate markers ...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Cytoplasmic DNA disclose high nucleotide diversity and different phylogenetic pattern in Taihangia rupestris Yu et Li
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Yueqin Cheng, Jingmian Duan, Zhenbin Jiao, G. Geoff Wang, Fengming Yan, Hongwei Wang Taihangia rupestris Yu et Li is an ancient species endemic to the Taihang Mountains, where it originated and evolved. Six chloroplast DNA (cpDNA) (trnT UGU -trnL UAA 5′exon, trnL UAA 5′exon-3′exon, trnL UAA 3′exon-trnF GAA , trnH GUG -trnK UUU , psbC-trnS and rps12-rpl20) and five mitochondrial DNA regions (rrn5/rrn18-2, nad1/2-3, nad4/3-4, nad7/1-2 and nad7/2-3) were employed to investigate the nucleotide diversity ...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

A set of microsatellite markers for population genetics of leopard cat (Prionailurus bengalensis) and cross-species amplification in other felids
We describe the isolation and characterization of novel microsatellite loci from the leopard cat, Prionailurus bengalensis Kerr, 1792 (Family Felidae). Using Illumina HiSeq2500 sequencing technology, we sequenced the leopard cat genome and identified 1.5 million loci of simple sequence repeats with di- to deca-nucleotide motifs. We developed twelve polymorphic markers with tetra-nucleotide motif types after screening 35 loci for amplification and polymorphism. The observed and expected heterozygosities of the markers were 0.438 and 0.423, respectively. The number of alleles per locus ranged from 2 to 7, with a mean polymor...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Characterization of pikeperch (Sander lucioperca) transcriptome and development of SSR markers
This study provides not only a valuable transcriptomic resource, but also a set of SSR markers for basic as well as applied research in pikeperch. (Source: Biochemical Systematics and Ecology)
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Non-concerted evolution in ribosomal ITS2 sequence in Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae)
In this study, we focused on ITS2 in Zanzibar tonguesole, Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae). Three types of ITS2 sequences (Type A, B, and C) coexisted and mainly differ in length, nucleotide diversity (π), secondary structure, and minimum free energy. Based on these different features, Type B and C were speculated as the putative pseudogenic ITS2 region. Moreover, Type C sequences were detected as recombinant from crossing over between Type A and B sequences. To our knowledge, this is the first report on ITS2 recombination in animal ribosomal RNA genes. The high degree of ITS2 sequence polymo...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

The isolation and characterization of a putative dehydrin gene in Triticum aestivum L.
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Yan Yu, Zaijun Yang Dehydrins (DHNs) are abundant, late embryonic proteins that are characterized by dehydrin domains that are involved in plant abiotic stress tolerance. In the current study, we report the cloning and characterization of a dehydrin gene (TaDhn33) in wheat (Triticum aestivum L.). The cDNA of TaDhn33, which was found to be 1217 bp in length, contains an 80-bp 5′-UTR and a 309-bp 3′-UTR. The open reading frame (ORF) of TaDhn33 was 828 bp and coded for a deduced protein of 275 amino acids. Th...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

A short phylogenetically informative cpDNA fragment for the identification of Pinus species
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Grigorios Georgolopoulos, Laura Parducci, Andreas D. Drouzas The genus Pinus L. consists of ca. 110 ecologically and economically important species extending from the arctic zone to the tropics. Nevertheless, there is little information in the literature on DNA-based methods for the identification of pine species. Here, we identified a new cpDNA fragment (trnV-H/x-h) able to differentiate among pine species and correctly depict the phylogeny within the genus. The fragment was identified based on PCR-RFLP profiles and primers d...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Sequestration of tropane alkaloids from Brugmansia suaveolens (Solanaceae) by the treehopper Alchisme grossa (Hemiptera: Membracidae)
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Carlos F. Pinto, Silvia Salinas, Luis Flores-Prado, Javier Echeverría, Hermann M. Niemeyer Treehoppers (Hemiptera: Membracidae) are sap-feeding insects distributed mainly in tropical regions. Alchisme grossa is a treehopper that has been reported in the Bolivian Yungas forests using mostly Brugmansia suaveolens (Solanaceae) as host-plant, where adult females oviposit and take care of their nymphs until they molt to adults. Brugmansia is a subtropical genus producing a variety of tropane alkaloids (TAs). We herein repo...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Genetic diversity in Tunisian perennial forage grasses revealed by inter-simple sequence repeats markers
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Nidhal Chtourou-Ghorbel, Nouha Ben Mheni, Hanen Elazreg, Salma Ghariani, Mohamed Chakroun, Neila Trifi-Farah The analysis of genetic variation within and among eight populations of perennial species Festuca arundinacea and Lolium perenne was based on 199 polymorphic inter-simple sequence repeat markers of which 49 (24.6%) were specific to perennial ryegrass, and 31 (15.5%) discriminate tall fescue. Shannon's index and AMOVA partition revealed that in each species the most ISSR variation occurred between populations, rather ...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

New reports on flavonoids, benzoic- and chlorogenic acids as rare features in the Psychotria alliance (Rubiaceae)
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Andreas Berger, Alexander Preinfalk, Wolfgang Robien, Lothar Brecker, Karin Valant-Vetschera, Johann Schinnerl Five flavonoid glycosides, three chlorogenic and one benzoic acid were isolated from leaves of seven species belonging to the genera Notopleura, Palicourea and Psychotria. In most species, common flavonol glycosides based upon quercetin and kaempferol were recorded, which corresponds well to literature data on other species of the Psychotria alliance. From Notopleura polyphlebia, however, the new dihydroflavonol gl...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Molecular characterization and gene evolution of the heat shock protein 70 gene in snakehead fish with different tolerances to temperature
In this study, a partial sequence of the heat shock protein 70 gene (HSP70) from the fish species Channa striatus was isolated and characterized. Evolutionary process that led to the diversity of HSP70 specific to vertebrates was also analysed. Results revealed that HSP70 is highly homologous in other fish families. The conservation of the HSP 70 gene among fish families could be driven by forces of natural selection due to climatic change. We exposed C. striatus to heat shock (32 °C) and cold shock (16 °C) respectively, in order to examine the differences of temperatures in influencing the expression pat...
Source: Biochemical Systematics and Ecology - May 19, 2016 Category: Biochemistry Source Type: research

Population genetics of the common long-armed octopus Octopus minor (Sasaki, 1920) (Cephalopoda: Octopoda) in Chinese waters based on microsatellite analysis
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Xiaolei Gao, Xiaodong Zheng, Qikang Bo, Qi Li Octopus minor (Sasaki, 1920) is a commercially important cephalopod in Chinese waters. To provide a theoretical basis for resource protection and sustainable management, we investigated genetic structure of ten O. minor populations in Chinese waters using microsatellite DNA markers. Eight microsatellite loci revealed high allelic diversity with 11–26 alleles per locus. Observed and expected heterozygosity varied from 0.412 to 0.900 and from 0.337 to 0.845, respectively. The ...
Source: Biochemical Systematics and Ecology - March 29, 2016 Category: Biochemistry Source Type: research

Phylogenetic and ancestral area reconstruction of Zingiberales from plastid genomes
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Jiabin Deng, Gang Gao, Yan Zhang, Fengmei He, Xuqiang Luo, Fengtai Zhang, Xinrong Liao, Khawaja Shafique Ahmad, Ruiwu Yang The Zingiberales is an ancient monocot order in the angiosperms. It has undergone radiation since the Cretaceous period. However, the relationships among primary lineages (families) are difficult to resolve. Additional support for phylogenetic relationships within this order have been obtained using plastid genome data from 76 coding genes and 4 rDNA loci from 17 species represented eight families. W...
Source: Biochemical Systematics and Ecology - March 29, 2016 Category: Biochemistry Source Type: research

Climate change may alter genetic diversity of Duchesnea indica, a clonal plant species
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Ji-Zhong Wan, Chun-Jing Wang, Chun-Xiang Liu, Hong-Li Li Climate change may alter the genetic diversity of plants. However, the relationship between genetic diversity in clonal plant species and climate change is unclear. To address this, we examined a representative clonal plant species, Duchesnea indica. We used microsatellite markers to analyze the genetic diversity of the species and used a correlation analysis to infer the relationship between climatic suitability and genetic diversity by using Maxent modeling. Then, we ...
Source: Biochemical Systematics and Ecology - March 27, 2016 Category: Biochemistry Source Type: research

Novel polymorphic microsatellite loci for a new target species, the sea cucumber Holothuria mammata
We report the development of 9 novel polymorphic microsatellites markers for Holothuria mammata and characterized them by testing in three different sample locations. All nine microsatellites revealed high polymorphism and diversity, with high number of alleles, ranged from 11 to 22 and expected heterozygosity, between 0.52 and 0.92. Significant genetic differentiation was found between populations. These microsatellites are providing valuable information which could be applied to fisheries management including, identification of stocks, assessment of their genetic diversity, estimation of gene flow and monitoring the fish...
Source: Biochemical Systematics and Ecology - March 25, 2016 Category: Biochemistry Source Type: research

Evidence of incomplete lineage sorting or restricted secondary contact in Lateolabrax japonicus complex (Actinopterygii: Moronidae) based on morphological and molecular traits
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Seung Eun Bae, Jin-Koo Kim, Jun Hyung Kim To clarify the taxonomic delimitation of the Lateolabrax japonicus complex, we conducted morphological and molecular analyses of 79 individuals collected from 10 localities in Korea. Assignment of individuals into three types (sea bass [SB], spotted sea bass [SSB] and intermediate sea bass [ISB]) was performed according to the presence/absence of black spots, and the distribution of black spots if present. Results of a canonical discriminant analysis showed that SB and ISB are closely ...
Source: Biochemical Systematics and Ecology - March 25, 2016 Category: Biochemistry Source Type: research

Chemical constituents from Lindera nacusua (D. Don) Merr
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Guo-Qing Wei, Jia-Sui Zhang, Jie-Ping Lei, Chao-Ying Ma, Yan Tong, He-Zhong Jiang This first phytochemical investigation on the roots of Lindera nacusua (D. Don) Merr led to the isolation of nine compounds, including demethylmacrosporine I (1), emodin-6-O-β-D-gluco- pyranoside (2), (−)-litsenolide D1 (3), (−)-(2Z,3R,4S)-2-(dodec-11-ynylidene)-3-hydroxy-4-methyilbu- tanolide (4), 1-O-3,4-dimethoxy-5-hydroxyphenyl-(6-O-3,5-dimethoxygalloyl)-β-d-glucopyranoside (5), 1-O-3,4-dimethoxy-5-hydroxyphenyl-(6-O-...
Source: Biochemical Systematics and Ecology - March 25, 2016 Category: Biochemistry Source Type: research

Multi-locus genomic analysis reveals the genetic diversity and population structure of the rock carp (Procypris rabaudi) in the upper Yangtze River
Publication date: June 2016 Source:Biochemical Systematics and Ecology, Volume 66 Author(s): Jun Song, Lijuan Chang, Dong Wang Rock carp [Procypris rabaudi (Tchang)] is an endemic species widely distributed throughout the upper reaches of the Yangtze River and its tributaries. Recently, the wild genetic resources of this species have markedly declined and it has been listed as vulnerable in China. Thus, conservation policies for this species are required urgently. However, information supporting decision-making on the conservation of this species is insufficient, especially at the genetic level. In this work, eight po...
Source: Biochemical Systematics and Ecology - March 25, 2016 Category: Biochemistry Source Type: research