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Atlantic Forest; Cariniana legalis; Jequitibá rosa; Microsatellites; Spatial genetic structure

The fragments of the Atlantic Forest of southern Bahia have a long history of intense logging and selective cutting. Some tree species, such as jequitibá rosa (Cariniana legalis), have experienced a reduction in their populations with respect to both area and density. To evaluate the possible effects of selective logging on genetic diversity, gene flow, and spatial genetic ... more

J.B. Leal; R.P. Santos; F.A. Gaiotto
Demographic changes; Genetic heterogeneity; Microsatellites; Mitochondrial sequences; Tayassu pecari

We sequenced the mitochondrial DNA (mtDNA) control region of 59 peccaries (44 white-lipped peccaries, Tayassu pecari, and 15 collared peccaries, Pecari tajacu). We also genotyped 3 DNA microsatellites from 78 white-lipped peccaries representing the 4 putative morphological subspecies (i.e., spiradens, aequatoris, pecari, and albirostris ... more

M. Ruiz-García; M. Pinedo-Castro; K. Luengas-Villamil; C. Vergara; J.A. Rodriguez; J.M. Shostell
Caldesia grandis; conservation genetics; Endangered species; Spatial genetic structure

The endangered marsh herb, Caldesia grandis, is native to China. We investigated the spatial structure of the genetic variation of three populations of C. grandis using RAPD markers and spatial autocorrelation analysis, based on the method of equal distance interval. A total of 157 individuals were sampled from four patches collected from the region of Hunan ... more

X.L. Yue; J.M. Chen; Y.H. Guo; Q.F. Wang
Cactaceae; Endangered species; Perfect microsatellite markers; Rare plants

The cactus genus Uebelmannia includes 3 narrow endemic species associated with rocky savanna habitats in eastern South America. Because of their rarity and illegal over-collection, all of these species are endangered. Taxonomic uncertainties resulting from dramatic local variation in morphology within Uebelmannia species preclude effective conservation efforts, such as ... more

E.M. Moraes; F.W. Cidade; G.A.R. Silva; M.C. Machado
Bromeliad differentiation; Endangered species; Molecular method

Bromeliaceae is an important botany family that includes many species with economic value; demand for members of this family is increasing. However, illegal collection frequently occurs, drastically reducing the species populations; thus, it is necessary to collect and store Bromeliaceae genetic material. In this study, we identified and quantified genetic variability of the Bromeliad ... more

S.D. Vieira; A.R.C. Rabbani; F. Santos; R. Silva-Mann; M.F. Arrigoni-Blank; A.P.N. Prata; L.V. Resende; M. Pasqual; A.F. Blank
Next-generation sequencing; Resequencing; Sequence variation; Toolkit

Large-scale next-generation sequencing (NGS)-based resequencing detects sequence variations, constructs evolutionary histories, and identifies phenotype-related genotypes. However, NGS-based resequencing studies generate extraordinarily large amounts of data, making computations difficult. Effective use and analysis of these data for NGS-based resequencing studies remains a difficult task ... more

W. He; S. Zhao; X. Liu; S. Dong; J. Lv; D. Liu; J. Wang; Z. Meng
Genetic variability; Korean threadsail filefish; Microsatellite loci; Next-generation sequencing; Stephanolepis cirrhifer

The threadsail filefish, Stephanolepis cirrhifer (Monacanthidae), is found mainly in the western Pacific. It is intensively caught in Korea and is a highly appreciated seafood delicacy. Consequently, the natural population of this species has drastically decreased, despite introductions from hatcheries. To provide information necessary for its conservation and management, we ... more

C.M. An; H.S. An; J.W. Lee; S.W. Hong
Ab initio methods; MicroRNAs; Next-generation sequencing; Pseudo hairpins; Secondary structure

MicroRNAs (miRNAs) are short, non-coding RNA molecules that play an important role in the world of genes, especially in regulating the gene expression of target messenger RNAs through cleavage or translational repression of messenger RNA. Ab initio methods have become popular in computational miRNA detection. Most software tools are designed to distinguish miRNA precursors from ... more

L.L. Hu; Y. Huang; Q.C. Wang; Q. Zou; Y. Jiang
marker-assisted selection; Next-generation sequencing; quantitative trait locus; Rice; Whole-genome resequencing

After complete sequencing of its genome and annotation of the majority of its ~32,000 genes, rice genome has become the model genome among the cereal genomes, and the focus has shifted from structural to functional genomics and application of genomic-derived information in rice breeding. During the past 2 decades, intensive worldwide efforts have led to significant improvements in rice. ... more

G. Li; S.W. Kwon; Y.J. Park
Aconitum austrokoreense; Endemic and endangered medicinal plant; Genetic diversity; Microsatellite marker; Next-generation sequencing

We used next-generation sequencing to develop 9 novel microsatellite markers in Aconitum austrokoreense, an endemic and endangered medicinal plant in Korea. Owing to its very limited distribution, over-harvesting for traditional medicinal purposes, and habitat loss, the natural populations are dramatically declining in Korea. All novel microsatellite markers were successfully ... more

Y.E. Yun; J.N. Yu; G.H. Nam; S.A. Ryu; S. Kim; K. Oh; C.E. Lim