Characterization of microsatellites and repetitive flanking sequences (ReFS) from the topmouth culter (Culter alburnus Basilewsky)

The topmouth culter (Culter alburnus) is an economically important freshwater fish in China. We obtained 159 microsatellite containing sequences (MCSs) from genomic DNA in this species enriched by (CAA)₈ and (GAA) ₈ probes. Careful examination of these sequences revealed the existence of cryptic repeated elements on presumed unique flanking regions. These cryptic elements can be grouped into three families, with the MCSs of the each family sharing regions of similarity ranging between 40 and 130 bp in length, with 96% sequence similarity. Repbase scans revealed that a large proportion of the cryptic repetitive DNA was identified as transposable elements (TEs). Complex patterns were apparent among these sequences. In most (89.2%), a single TE was identified in an MCS, in three instances, the same TE was observed twice in the same MCS. Some MCS have two or even four different TEs. We isolated nine polymorphic microsatellite loci from sequences with no matches to TEs. In a sample of 30 cultured C. alburnus, we found that the average allele number was 8.1 per locus (range = 4–17), with polymorphism informative content ranging from 0.364 to 0.898. These microsatellites can be used to study the population genetic diversity of this species.     

Assessing genetic diversity of populations of topmouth culter (Culter alburnus) in China using AFLP markers

Genetic diversity of five wild populations and a cultured population of topmouth culter (Culter alburnus) was investigated using amplified fragment length polymorphism (AFLP). A total of 373 reproducible bands amplified with seven AFLP primer combinations were obtained from 163 fish. The percentage of polymorphic loci ranged widely from 37.0% to 69.2% within distinct populations. The cultured population appeared to have a lower level of polymorphism (37.0%), gene diversity (0.121 ± 0.188) and Shannon's Information index (0.183 ± 0.263) than the wild populations. Analysis of molecular variance (AMOVA) revealed that average F_ST value overall loci was 0.2671, and the percentage of variation within population (73.29%) was larger than among populations (26.71%) (P < 0.01). The six populations were clustered into two major clades with UPGMA. The results from analysis of population pairwise gene flow indicated moderate gene flow among populations. Our study indicated that the genetic diversity of the cultured population was reduced compared with the wild populations. Geographic isolation, habitat, and artificial selection all may have played important roles in population differentiation. The information may be beneficial to future broodstock selection and defining conservation management for the different populations of topmouth culter.     

Genetic diversity of golden takin (Budorcas taxicolor bedfordi) population from Qinling Mountains in China revealed by sequence analysis of mitochondrial DNA control region

The golden takin is an endangered species, listed as a First Grade Protected animal and found only in the Qinling Mountains in China. A great deal of research on the golden takin's living habitat, population size, and home range has been conducted. Here, we employed sequence analysis of the mitochondrial DNA control region to study the genetic diversity of the golden takin from three separate nature reserve parks in the Qinling Mountains. We also compared the results of our study with previously published data on the genetic diversity of mixed takin species located in the Qinling Mountains and the Minshan area. Based on 62 sampled golden takin individuals, we found an overall mean genetic haplotype diversity of 0.687. There is no significant geographic genetic diversity across different golden takin populations within the Qinling Mountains. However, we did show significant diversity between golden takin from the Qinling Mountains and from Minshan. These original data provide a foundation for the genetic diversity of golden takin, and will yield comprehensive information for better supporting the management in the national reserve parks.     

Comparative analysis of the complete mitochondrial genomes of three geographical topmouth culter (Culter alburnus) groups and implications for their phylogenetics

Topmouth culter (C. alburnus) is an important commercial fish in China. We compared the nucleotide variations in the mtDNA genomes among three geographical groups of Culter alburnus: Liangzi Lake, Hubei Province (referred to as LZH); Taihu Lake, Jiangsu Province (TH); and Poyang Lake, Jiangxi Province (PYH). The similarity of whole mtDNA genomes ranged from 0.992 to 0.999. The similarity among 13 protein-coding genes, 2 rRNA genes, and the D-loop sequences was found to range from 0.982 to 0.996. This is useful data for future designing work for making specific molecular marker for distinguishing individuals of C. alburnus from the three geographical groups. An extended termination-associated sequence (ETAS) and several conserved blocks (CSB-F, CSB-E, CSB-D, CSB1, CSB2, and CSB3) were identified in the mtDNA control regions. A phylogenetic analysis shows a monophyletic relationship of the LZF-female and the LZF-male. However, the analysis also showed paraphyletic relationships for the other two geological groups. This result will be useful for the future breeding work of C. alburnus.     

Genetic diversity analysis of Topmouth Culter (Culter alburnus) based on microsatellites and D-loop sequences

Environmental Biology of Fishes - Topmouth culter (Culter alburnus) is an economically important fish species distributed in rivers, lakes and reservoirs throughout China. This study focused on the...     

Chromosome-level genome assembly and whole-genome resequencing of topmouth culter (Culter alburnus) provide insights into the intraspecific variation of its semi-buoyant and adhesive eggs

Topmouth culter (Culter alburnus) is an ecologically and economically important species belonging to the subfamily Culterinae that is native to and widespread in East Asia. Intraspecific variation of semi-buoyant and adhesive eggs in topmouth culter provides an ideal opportunity to investigate the genetic mechanisms of spawning habits underlying the adaptive radiation of cyprinids in East Asia. In this study, we present a chromosome-level genome assembly of topmouth culter and re-sequenced 158 individuals from six locations in China covering three geographical groups and two egg type variations. The topmouth culter genome size was 1.05 Gb, with a contig N50 length of 17.8 Mb and anchored onto 24 chromosomes. Phylogenetic analysis showed that the divergence time of the Culterinae was coinciding with the time of initiation of the Asian monsoon intensification. Gene family evolutionary analysis indicated that the expanded gene families in topmouth culter were associated with dietary adaptation. Population-level genetic analysis indicated clear differentiation among the six populations, which were clustered into three distinct clusters, consistent with their geographical divergence. The historical effective population size of topmouth culter correlated with the Tibetan Plateau uplifting according to the demographic history reconstruction. A selective sweep analysis between adhesive and semi-buoyant egg populations revealed the genes associated with the hydration and adhesiveness of eggs, indicating divergent selection towards different hydrological environments. This study offers a high-resolution genetic resource for further studies on evolutionary adaptation, genetic breeding and conservation of topmouth culter, providing insights into the molecular mechanisms for egg type variation of East Asian cyprinids.     

Fatty acid profiles of the topmouth culter (Culter alburnus Basilewsky, 1855) from five lakes located at different latitudes in China

The topmouth culter (Culter alburnus Basilewsky, 1855) is a freshwater carnivorous fish of high nutritional value and widely distributed in lakes and reservoirs of China. In order to evaluate the fatty acid profiles in relation to habitat characteristics and to elucidate the main composition predictors, C. alburnus were collected from five lakes (Xingkai‐ LXk, Hongze‐ LHz, Kuilei‐ LKl, Chidong‐ LCd and Dongting‐ LDt) in China, ranging in latitudes from 28°30′ to 44°44′N and altitudes from 4 to 64 m. Ten fish from each lake ranging in total lengths from 414.2 to 423.9 mm were sampled between May to June in 2013 and 2014. A total of 23 fatty acids were identified using gas chromatography. Fatty acids that predominated in muscle samples of the fish were 16:0, 18:0, 16:1n?7, 18:1n?9, 20:5n?3, 22:6n?3 and 20:4n?6. Important differences in the fatty acid profiles of fish from high and low latitude lakes were discernible in that the two high latitudinal lakes (LXk and LHz) had significantly higher (p < .05) ratios of n?3 to n?6 fatty acids and levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), than those fishes in the low latitudinal lakes (LKl, LCd and LDt); these observations were confirmed by a principal component analysis. Therefore, it appears that multivariate analysis enables to distinguish fish from different lakes based on their characteristic fatty acid signatures; this would make a contribution to fish product traceability. The percentages of total saturated fatty acids increased significantly with increasing ambient temperature, and lakes at lower latitudes had higher levels of 17:0, 18:0, 18:2n?6, 20:3n?6 and lower levels of 16:1n?7 and 18:1n?9. Theoretical information criteria showed that the percentage of total saturated fatty acids varied more with temperature than with latitude and that this temperature‐dependent variation is nonlinear. Variation partitioning shows that most of the geographical variations are not only due to the nonlinear effects of temperature but also to the independent effects of the lake features. By contrast, no significant variations in fish lengths were found.     

Patterns of genetic variation in the Chinese endemic Psilopeganum sinense (Rutaceae) as revealed by nuclear microsatellites and chloroplast microsatellites

Psilopeganum sinense is a perennial herb endemic to Three-Gorges Reservoir Area (TGRA) in China. Genetic diversity of this endangered species was assessed by using 11 nuclear microsatellites and three chloroplast microsatellite (cpSSR) markers. A total of 8 haplotypes were identified in a survey of 212 individuals sampled from nine populations encompassing most of the natural range of the species. A low level of genetic diversity was detected: H_E = 0.301 for SSR and H_E = 0.28 for cpSSR. Populations were highly differentiated from one another: an AMOVA analysis that showed that 56.3% and 68.2% genetic variation resided between populations based on SSR and cpSSR analysis, respectively, and F_ST and F_STc (0.467 for SSR and 0.644 for cpSSR, respectively) were high. Significant differences were found between estimates of haplotypic differentiation calculated by using unordered alleles (G_STc = 0.857) and ordered alleles (N_STc = 0.728), which indicated the existence of phylogeographical structure in P. sinense. The indirect ratio of pollen flow/seed flow derived from estimates of haplotypic and nuclear DNA differentiation indicated that gene flow via pollen is less efficient than via seed. Two distinct evolutionary lineages (evolutionary significant units, ESUs) were recognized for P. sinense on the basis of both the PCoA and NCA analysis. Sampling strategies for conserving this endangered plant were discussed.     

黄山短尾猴mtDNA控制区序列变异及种群的遗传多样性

短尾猴属灵长目(Primates)猴科(Cercopithecidae)猕猴属(Macaca),是我国特有的国家二级保护动物。为了更有效地保护其野生种群,本文研究了黄山短尾猴种群内的遗传多样性,并对黄山短尾猴与四川短尾猴种群间的遗传差异进行了分析。共测定了黄山短尾猴7个群体中的30个样本的mtDNA控制区5′端493bp的序列,只发现了7个变异位点,定义了3种单倍型,单倍型序列之间缺乏变异,种群中的核苷酸多样性很低(0.006);3种单倍型相应地将黄山种群分为了3个亚群,不同亚群之间呈现出一定的片断化分布,从分子水平上初步揭示了短尾猴黄山种群的遗传多样性。与四川短尾猴的相应序列比较,黄山短尾猴控制区序列存在很大差异,共有59个变异位点,而且存在大片段的碱基插入/缺失,有78%的遗传变异发生在两个种群之间,两个种群间的核苷酸歧异度已达8.21%。进一步分析表明,黄山短尾猴与四川短尾猴之间存在着极显著的遗传分化(FST=0.399,P<0.001),基于最大似然法和邻接法构建的系统发生树均将两者聚为不同的类群,支持将它们归入各自的管理单元。     

Genetic population structure of miiuy croaker (Miichthys miiuy) in the Yellow and East China Seas base on mitochondrial COI sequences

The miiuy croaker (Miichthys miiuy) is an economically important fish species in China. However, information about population structure in this species is limited. In this study, the genetic diversity and population structure of four populations of Miichthys miiuy were investigated using a mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) segment of 599 bp. A total of 35 polymorphic sites, and 31 haplotypes were defined in 109 individuals. High levels of haplotype diversity (0.731 ± 0.047) and low nucleotide diversity (0.00278 ± 0.0019) were observed in miiuy croaker populations. The results of AMOVA and pairwise fixation index (F_ST) analysis did not indicate any significant genetic differentiation among populations obtained from four sites (P > 0.05). In addition, no significant genealogical branches or clusters were recognized in the NJ tree. Analysis of neutral evolution and mismatch distribution suggested that the miiuy croaker might have experienced a recent population expansion.     

Siberian wild rye (Elymus sibiricus L.): Genetic diversity of germplasm determined using DNA fingerprinting and SCoT markers

Elymus sibiricus is a perennial, self-pollinating, allotetraploid grass native to northern Asia. It is widely used in cultivated pastures and natural grassland due to excellent cold and drought tolerance, good forage quality, and adaptability to a variety of habitats. Information on the genetic diversity and variation among worldwide E. sibiricus germplasm is limited but necessary for germplasm collection, conservation and effective commercial use. In this study we ana lyzed genetic diversity and variation of 69 E. sibiricus accessions from the species range and constructed DNA fingerprinting profiles of 24 accessions using SCoT markers. A total of 173 bands were generated from 16 SCoT primers, 154 of which were polymorphic with 89.0% of polymorphic bands (PPB) occurring at the species level. The PPB within 8 geographical regions ranged from 2.3 to 54.3 %. Genetic variation was greater within geographical regions (57.9%) than between regions (42.1%). The 24 accessions from Qinghai-Tibet Plateau, Mongolia Plateau, Kazakhstan, and Russia were distinguished by their unique fingerprinting. This is the first report using SCoT markers for identifying cultivars and accessions of E. sibiricus. The DNA fingerprinting profiles of E. sibiricus were useful in germplasm collection and identification. The genetic diversity of worldwide E. sibiricus germplasm has been substantially affected by ecogeographical factors. Our results suggest that collecting and evaluating E. sibiricus germplasm from major geographic regions and unique environments broadens the available genetic base and illustrates the range of variation.     

Detection of genetic diversity in closely related bread wheat using microsatellite markers

Wheat microsatellites (WMS) were used to estimate the extent of genetic diversity among 40 wheat cultivars and lines, including mainly European elite material. The 23 WMS used were located on 15 different chromosomes, and revealed a total of 142 alleles. The number of alleles ranged from 3 to 16, with an average of 6.2 alleles per WMS. The average dinucleotide repeat number ranged from 13 to 41. The correlation coefficient between the number of alleles and the average number of repeats was only slight (r _s = 0.55). Based on percentage difference a dendrogram is presented, calculated by the WMS-derived data. All but two of the wheat cultivars and lines could be distinguished. Some of the resulting groups are strongly related to the pedigrees of the appropriate cultivars. Values for co-ancestry (f) of 179 pairs of cultivars related by their pedigrees (f0.1) averaged 0.29. Genetic similarity (GS) based on WMS of the same pairs averaged 0.44. The rank correlation for these pairs was slight, with r _s = 0.55, but highly significant (P<0.001). The results suggest that a relatively small number of microsatellites can be used for the estimation of genetic diversity and cultivar identification in elite material of hexaploid bread wheat.     

Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon

In order to determine how informative a set of microsatellites from tomato is across the genus Lycopersicon, 17 microsatellite loci, derived from regions in and around genes, were tested on 31 accessions comprising the nine species of the genus. The microsatellite polymorphisms were used to estimate the distribution of diversity throughout the genus and to evaluate the efficacy of microsatellites for establishing species relationships in comparison with existing phylogeny reconstructions. Gene diversity and genetic distances were calculated. A high level of polymorphism was found, as well as a large number of alleles unique for species. The level of polymorphism detected with the microsatellite loci within and among species was highly correlated with the respective mating systems, cross-pollinating species having a significantly higher gene diversity compared to self-pollinating species. In general, microsatellite-based trees were consistent with a published RFLP-based dendrogram as well as with a published classification based on morphology and the mating system. A tree constructed with low-polymorphic loci (gene diversity <0.245) was shown to represent a more-reliable topology than a tree constructed with more-highly polymorphic loci. Received: 19 February 2001 / Accepted: 26 March 2001     

Molecular characterization of trypsinogens and development of trypsinogen gene expression and tryptic activities in grass carp (Ctenopharyngodon idellus) and topmouth culter (Culter alburnus)

This study examined the gene structures and expression of trypsinogens, as well as the trypsin activities of the grass carp Ctenopharyngodon idellus (herbivorous) and the topmouth culter Culter alburnus (carnivorous), which are commercially important freshwater species of the family Cyprinidae in China. Isolated full-length trypsinogen cDNA clones were 869 bp and 857 bp. The deduced amino acid sequences were 242 aa and 247 aa long, both containing the highly conserved residues essential for serine protease catalytic and conformational maintenance. The results from isoelectric and phylogenetic analyses suggest that grass carp trypsinogen is grouped with teleost trypsinogen group I, while topmouth culter trypsinogen is grouped with group II. The expression pattern of trypsinogen mRNA was similar between these two species, appearing 2 days post-hatching (dph) and reaching peaks at 11 and 23 dph. The trypsin-specific activities in both species were detected 2 dph and reached the major peaks at 8 dph, however the minor peaks were observed at 20 dph in the grass carp and 17 dph in the topmouth culter. The trypsin-specific activity was significantly higher in the grass carp than in the topmouth culter, which may be attributed to the nature of their different nutritional habits.     

Genetic diversity of cultured populations of giant freshwater prawn (Macrobrachium rosenbergii) in China using mtDNA COI and 16S rDNA markers

Partial sequences of mitochondrial DNA 16S rDNA and COI genes (395 bp and 498 bp respectively) were sequenced from samples of ten cultured populations of Macrobrachium rosenbergii (Giant Freshwater Prawn – GFP) in Zhejiang, Guangdong and Guangxi Provinces in China and two wild populations of GFP from Mekong River and Dongnai River in Viet Nam. Five haplotypes of 16S rDNA were identified in the 360 samples. The wild populations displayed nucleotide diversity (π) of 0.0008 and 0.0003, and genetic diversity (h) of 0.3030 and 0.1310 in the Mekong River and Dongnai River respectively. The cultured populations displayed no significant genetic diversity. COI sequences identified 17 haplotypes based on 21 polymorphic sites. At this marker, the 12 populations showed a range of h from 0.1290 to 0.6940 and π from 0.0003 to 0.0073. The largest genetic distance (Da) among the 12 populations was 0.0065 (between ZJB and BT/DN populations) and the lowest Da was 0.0003 (between GDD and GDA populations). The wild populations had higher genetic diversity than the cultured populations, but three of cultured populations from Zhejiang (ZJA, ZJB and ZJC) had π higher than wild populations, because they originated from Thailand, Bangladesh and the Mekong River in Viet Nam.     

Microsatellite diversity and population genetic structure of redfin culter ( Culter erythropterus ) in fragmented lakes of the Yangtze River

Redfin culter (Culter erythropterus) is a small lethic freshwater fish and widely distributed in the adjacent lakes of the Yangtze River of China. Five microsatellite loci were applied to investigate the genetic variation and population structure of redfin culter from seven lakes in the middle-and-lower reaches of the Yangtze River. The gene diversity was high among the populations (H > 0.9), the average number of alleles among seven populations was low with a range from 2.00 to 3.87. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.111 to 0.419 and from 0.162 to 0.750, respectively. Significant deviations from Hardy-Weinberg Equilibrium expectation were found in 50% of the total locus-population combination tests in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percentage of variance among and within these populations were 6.18 and 93.82, respectively. The Fst values (0.062, P < 0.001) among studied populations indicated that there were significant genetic differentiations among redfin culture populations from the scattered lakes with different connections to the Yangtze River. These results are useful for the evaluation and conservation of small freshwater fishes. The factors that may be involved in low intra-population polymorphism and the pattern of the population genetic structure of redfin culter from the Yangtze River were discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: C. Sturmbauer     

西藏牦牛线粒体DNA 的遗传多样性及系统进化分析

为从分子水平上探究西藏牦牛类群的遗传多样性、亲缘关系,本研究测定了日多牦牛、类乌齐牦牛、丁青牦牛、错那牦牛、隆子牦牛、仲巴牦牛、聂荣牦牛、申札牦牛等8 个西藏牦牛类群共328 头牦牛mtDNAD-loop区序列,分析其多态性,构建系统进化树。结果表明:本次测定的西藏牦牛mtDNA D-loop 区序列长度为 887 - 895 bp,共检测到135 个变异位点,其中单态突变位点52 个,简约信息位点83 个。在328 个个体中共检测出91 种单倍型,平均单倍型多样性(Hd)、平均核苷酸多样性(π)分别为0. 884、0.010 27,显示西藏牦牛具有丰富的遗传多样性。8 个类群间平均遗传距离为0.011;日多牦牛与错那牦牛间遗传距离最小(0. 006);类乌 齐牦牛与隆子牦牛间遗传距离最大(0.015)。系统进化分析显示西藏牦牛可分为两大类,错那牦牛是较纯的牦牛类群,其它牦牛类群在进化过程中出现相互交流的情况。     

Determination of genetic diversity of the cuttlefish Sepiella japonica inhabiting Chinese coastal waters using the mitochondrial D-loop region: The valuable inspiration to artificial releasing project

The cuttlefish Sepiella japonica, was once one of the four major marine fisheries of China and has dramatically declined since the 1980s to near extinction. The artificial releasing project was launched for resource restocking since 2006. Aiming to provide some valuable information to the management of the releasing project, the mitochondrial DNA control region sequence was employed to assess the genetic variation of various geographical populations in present study. The genetic diversity of S. japonica was characterized with the low value of nucleotide diversity (0.00313 ± 0.070). Pairwise fixation index (Fst) analysis indicated insignificant genetic differentiation among southern populations (p > 0.05). However, the QD population showed the significant genetic differention with other populations (p < 0.05). The highest genetic diversity was detected in ND population and was recommended to be the germplasm resources for artificial releasing project. In summary, the presented results provided some new information for genetic assessment in this study that would be crucial for establishing effective releasing strategies for this species.     

Studies on genetic diversity and phylogenetic relationships of limpograss (Hemarthria altissima) and related species based on combined chloroplast DNA intergenic spacer data

Hemarthria R. Br. is a genus which includes important forage grasses. However, there is currently a lack of data analysis on the chloroplast DNA (cpDNA) of Hemarthria species. This study is to use three cpDNA intergenic spacers (trnL-F, trnC-ycf6 and psbC-trnS) to obtain phylogenetic information in 36 Hemarthria samples including four Hemarthria species: Hemarthria altissima (Poir.) Stapf et C. E. Hubb., Hemarthria compressa (L. f.) R. Br., Hemarthria uncinata R. Br., and Hemarthria japonica (Hack.) Roshev. Data analysis revealed that non-significant genetic diversity existed in our samples, which was implied by nucleotide sequences information and the results of haplotypic and nucleotide diversity. The results of phylogenetic trees based on maximum likelihood (ML) and Bayesian inference (BI) revealed that H. altissima and H. compressa samples were not entirely distinct, suggesting that the two species share an intimate genetic relationship. A haplotype median-joining (MJ) network revealed broadly similar results to those derived from the ML and BI trees and implied that haplotype H3 may represent an ancient haplotype. Analysis of the population statistic F_ST revealed little genetic differentiation among the seven populations of H. altissima in Africa.