Showing papers in "Conservation Genetics Resources in 2016"
TL;DR: It is confirmed that eDNA can be applied to detect burrowing aquatic freshwater crayfish without disturbing their habitats and evaluated the species distributions with comparing hand-capture method in the headwater streams.
Abstract: The freshwater crayfish, Cambaroides japonicus, is endangered in Hokkaido, Japan and inhabits burrows. Here, we applied environmental DNA (eDNA) method for evaluating the species distributions with comparing hand-capture method in the headwater streams. We detected the eDNA of C. japonicus from all sites, where we collected C. japonicus, and confirmed that eDNA can be applied to detect burrowing aquatic freshwater crayfish without disturbing their habitats.
63 citations
TL;DR: The impact primer design may have on eDNA applications in general and future considerations for conservation efforts with the Yangtze finless porpoise are summarized and suggested.
Abstract: Environmental DNA (eDNA) represents a sensitive and efficient method for noninvasively sampling rare or otherwise hard to monitor taxa, potentially making it a powerful tool for conservation management. Still, this novel method can be affected by sampling protocols, abiotic characteristics of the microhabitat, the focal taxa itself, and primer design. Here we designed 12 species-specific primers for the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) inhabiting the middle to lower Yangtze River in China to enable complementary population survey tools for conservation efforts. Representing primer pairs that amplify a range of DNA fragment sizes, we test these primers for sensitivity at amplifying finless porpoise DNA using conventional PCR from serial diluted blood samples, and from eDNA in aquaria and in the wild, including a nature reserve and a negative control site. We further investigated the capacity for these primers to detect finless porpoise DNA signals from water samples over a 30-day period. Our study presents which primers were successful at amplifying finless porpoise DNA from aquaria and in the wild, and further demonstrates no significant amplicon size effects on primer sensitivity or longevity. We summarize the impact primer design may have on eDNA applications in general and suggest future considerations for conservation efforts with the Yangtze finless porpoise.
37 citations
TL;DR: A quantitative PCR assay was developed to detect the presence of Arctic grayling DNA in environmental samples and amplified low concentrations of Arcticgrayling DNA consistently, and did not amplify non-target species, including sympatric salmonid fishes.
Abstract: The upper Missouri River basin in the northwestern US contains disjunct Arctic grayling (Thymallus arcticus) populations of conservation concern. To assist efforts aimed at understanding Artic grayling distribution, we developed a quantitative PCR assay to detect the presence of Arctic grayling DNA in environmental samples. The assay amplified low concentrations of Arctic grayling DNA consistently, and did not amplify non-target species, including sympatric salmonid fishes.
36 citations
TL;DR: A bioinformatics pipeline for microsatellite development from Illumina paired-end sequences is developed, which is packaged in the open-source bio informatics tool Galaxy and provides a user-friendly graphical user interface.
Abstract: Microsatellites are useful tools for ecologists and conservationist biologists, but are taxa-specific and traditionally expensive and time-consuming to develop. New methods using next-generation sequencing (NGS) have reduced these problems, but the plethora of software available for processing NGS data may cause confusion and difficulty for researchers new to the field of bioinformatics. We developed a bioinformatics pipeline for microsatellite development from Illumina paired-end sequences, which is packaged in the open-source bioinformatics tool Galaxy. This optimises and streamlines the design of a microsatellite panel and provides a user-friendly graphical user interface. The pipeline utilises existing programs along with our own novel program and wrappers to: quality-filter and trim reads (Trimmomatic); generate sequence quality reports (FastQC); identify potentially-amplifiable microsatellite loci (Pal_finder); design primers (Primer3); assemble pairs of reads to enhance marker amplification success rates (PANDAseq); and filter optimal loci (Pal_filter). The complete pipeline is freely available for use via a pre-configured Galaxy instance, accessible at https://palfinder.ls.manchester.ac.uk.
33 citations
TL;DR: A new pair of primers are developed for efficient and affordable high-throughput analysis of a 250 base pair stretch of DNA from the mitochondrial 16S rRNA gene of vertebrates, especially amphibians and fishes, by adapting a double-indexed protocol for Illumina platforms.
Abstract: Metabarcoding is a promising tool for biodiversity inventories and other applications in conservation genetics. We developed a new pair of primers for efficient and affordable high-throughput analysis of a 250 base pair stretch of DNA from the mitochondrial 16S rRNA gene of vertebrates, especially amphibians and fishes. By adapting a double-indexed protocol for Illumina platforms, our approach allows pooling of hundreds of samples in a single sequencing run. We obtained high detection rates of 82–93 % for fish in two German streams, 70 % for mock mixes of DNA from amphibians and fishes, and could distinguish multiple gene copies in amphibians, probably caused by nuclear-mitochondrial transposed DNA or heteroplasmy.
30 citations
TL;DR: The chloroplast genome of A. quinata is reported by Illumina pair-end sequencing, finding that it encodes 113 different genes, including 79 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs.
Abstract: Akebia quinata is an over-harvesting shrub which faces an urgent need for reasonable conservation strategies. In this study, we report its complete chloroplast genome by Illumina pair-end sequencing. The total cp genome size was 157,817 bp in length, containing a pair of inverted repeats of 26,143 bp, separated by large single copy and small single copy of 86,543 bp and 18,988 bp, respectively. The chloroplast genome of A. quinata encodes 113 different genes, including 79 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs. A total of 47 perfect cp microsatellites were analyzed in the A. quinata. The majority of the SSRs in this cp genome are mononucleotides (74.47 %). Regions of the highest variability were sought out by comparing with A. trifoliate. There are only 385 nucleotide substitutions and 141 indels between the two genomes. Six highly variable regions were identified including four intergenic regions and two coding regions.
20 citations
TL;DR: The present study developed 46 novel SNP markers based on transcriptome of H. erectus that can provide an effective tool for population study and genetic breeding.
Abstract: The population of lined seahorse (Hippocampus erectus) rapidly reduced because of the heavy exploitation in the wild. The single nucleotide polymorphism (SNP), known as one of the popular third-generation molecular markers can be developed easier and faster from high-throughput transcriptome sequencing. In this study, we developed 46 novel SNP markers based on transcriptome of H. erectus. Genetic diversity analysis showed that observed heterozygosity (Ho) and expected heterozygosity (He) were varied from 0.1724 to 0.5250 and from 0.1588 to 0.5000, respectively, and the minor allele frequency value was from 0.0625 to 0.5000. Seven loci were significantly different from Hardy–Weinberg equilibrium (P < 0.05) and significant linkage disequilibrium occurred between HeSNP24 and HeSNP38 (P < 0.01). The present study can provide an effective tool for population study and genetic breeding.
19 citations
TL;DR: The evidence suggests that heterogeneity in Ne can be just as important as heterogeneity in mutation rates in determining levels of genetic diversity throughout the genome, and potential implications for conservation and breeding practices are discussed.
Abstract: Effective population size (N
e
) is defined as the size of an idealized population undergoing the same rate of genetic drift as the population under study. It is a central concept in population genetics and used extensively in the design and monitoring of conservation and breeding programs. It is most often assumed that genetic drift effects are homogeneous across the genome and thus, so is N
e
. However, theory predicts that various processes can modify rates of genetic drift experienced by a locus in the genome. In particular, selection affecting linked neutral sites and rates of recombination can modulate the intensity of genetic drift throughout the genome. The increasing availability of sequence data has made it possible to test whether
a single N
e
can account for the evolution of the genome. In this article, we discuss reasons why a heterogeneous N
e
can be expected theoretically and review what evidence is available from empirical studies. We finish by discussing potential implications for conservation and breeding practices. The evidence suggests that heterogeneity in N
e
can be just as important as heterogeneity in mutation rates in determining levels of genetic diversity throughout the genome.
19 citations
TL;DR: The ability to detect C. pecorum and KoRV in DNA isolated from koala scats is demonstrated and will be useful for studying the prevalence, transmission and impact of these pathogens in wild populations which may subsequently inform conservation management strategies.
Abstract: Pathogenic diseases may threaten the viability of wild animal populations, especially when already vulnerable. The mitigation of risks associated with pathogenic infections in populations is an important factor in conservation strategies. Koalas are of conservation concern across the north of their range and are affected by two main pathogens; Chlamydia pecorum and the koala retrovirus (KoRV). This study tested whether DNA from C. pecorum and KoRV could be detected in genetic material isolated from koala scats. Detection of C. pecorum in scat isolated DNA samples was compared with results obtained from urogenital swabs collected from the same individuals as part of an independent study. The ability to detect KoRV in scats from both northern and southern regions of the koala’s range was also assessed. There was a high level of concordance (5/6) between the detection of C. pecorum in DNA isolated from scats and urogenital swabs from the same individual. In positive samples, C. pecorum ompA genotypes were identical between DNA from scats and urogenital swabs in two out of three cases. In samples from the south of the koala’s range, KoRV copy number was higher in DNA isolated from scats compared to DNA isolated from ear tissue, potentially indicating the detection of horizontally acquired infections. Our results demonstrate the ability to detect C. pecorum and KoRV in DNA isolated from koala scats. This method will be useful for studying the prevalence, transmission and impact of these pathogens in wild populations which may subsequently inform conservation management strategies.
19 citations
TL;DR: The authors' results showed useful genomic resources for pacu, with applicability in conservation purposes and aquaculture industry by using SNPs markers, and some of them related to immune system genes.
Abstract: Pacu (Piaractus mesopotamicus) is a Neotropical freshwater fish threatened by overfishing, and one of the species of highest commercial value for aquaculture. Genetic variability analysis through molecular markers is an essential technique to genetic management of the wild and cultivated stocks. The main objective of this study was to identify and validate gene-associated SNPs of the liver transcriptome of pacu. Through genetic analysis in one natural population (Parana River), 32 polymorphic SNPs were successfully genotyped and validated, some of them related to immune system genes. The observed and expected heterozygosity ranged from 0.059 to 0.706 and 0.058 to 0.507, respectively. All loci were in Hardy–Weinberg equilibrium (P > 0.05). Our results showed useful genomic resources for pacu, with applicability in conservation purposes and aquaculture industry by using SNPs markers.
18 citations
TL;DR: The complete mitochondrial genomes for the Argentine ant Linepithema humile and the little fire ant Wasmannia auropunctata are reported, finding that these two globally invasive ants are more related to those taxa of the subfamilies Formicinae and Myrmicinae than to the consubfamilial Leptomyrmex pallens.
Abstract: Ants are among the most widespread and damaging of invasive alien species. Here, we report the complete mitochondrial genomes for two globally invasive ants: the Argentine ant Linepithema humile and the little fire ant Wasmannia auropunctata. The circular genomes of L. humile and W. auropunctata are 15,929 and 16,362 bp in length, respectively, and encode the same typical set of 37 mitochondrial genes (i.e. 13 PCGs, 22 tRNAs and two rRNAs) and one control region. The mitochondrial genome of W. auropunctata harbors a unique gene arrangement (‘rrnS-trnV-CR-trnM-trnI-trnQ-nad2-trnW-trnC-trnY’; the underlines indicate inverted genes) between rrnL and cox1. Phylogenetic analysis largely corroborated the traditional taxonomy, except for L. humile which was found to be more related to those taxa of the subfamilies Formicinae and Myrmicinae than to the consubfamilial Leptomyrmex pallens. Our genomic data can be readily used for genetic assays of these two globally invasive ants.
TL;DR: This assay will prove useful for low-density detection of P. fluviatilis to assist in the management of this invader, with conservation benefits for the native species it threatens.
Abstract: Invasive alien species are one of the leading causes of extinctions worldwide. Preventing their establishment, eradicating or containing their spread relies on low-density detection. Environmental DNA (eDNA) has been shown to have superior detection sensitivity compared to traditional methods, permitting detection at lower densities. Here, we develop a species-specific assay to detect Perca fluviatilis (redfin perch), an invasive freshwater fish present in Australia. We show that the assay is highly sensitive and highly specific to detect the species in Australian freshwater environments and demonstrate the utility of the assay for detecting the species from environmental water samples. This assay will prove useful for low-density detection of P. fluviatilis to assist in the management of this invader, with conservation benefits for the native species it threatens.
TL;DR: This study evaluates the quality of naturally shed macaw feathers in tropical environmental conditions and presents new primers for molecular sexing on the feather samples and successfully validated 11 microsatellite markers for use in genetic tagging studies on large macaws.
Abstract: Genetic tagging is the unique identification of individuals by their DNA profile. This technique is well established in mammals, but it has not yet been widely adopted for birds. Extraction methods for minute amounts of DNA even enable the use of genetic tagging from non-invasive samples, like hair, scat, or feather. In this study, we evaluate the potential for non-invasive genetic tagging by using molted feathers of two sympatric macaw species in the Peruvian Amazon. Correct species identification is critical when relying on feathers for genetic analysis, so we describe multilocus methods for species identification. We evaluate the quality of naturally shed macaw feathers in tropical environmental conditions and present new primers for molecular sexing on the feather samples. We successfully validated 11 microsatellite markers for use in genetic tagging studies on large macaws and confirmed that DNA from blood and feather samples yields equivalent population genetic patterns. The techniques described here can be implemented for other birds with higher conservation concern.
TL;DR: 182 SNP markers were developed for Ayous by incorporating information from two next generation sequencing approaches into a single genotyping panel for MassARRAY® iPLEX™ and successfully used to genotype 753 individuals from 43 populations in five Tropical West and Central African Countries.
Abstract: 182 SNP markers were developed for Ayous (Triplochiton scleroxylon K. Schum) by incorporating information from two next generation sequencing approaches (RADseq Floragenex and AFLPseq IonTorrent PGM) into a single genotyping panel for MassARRAY® iPLEX™. This set of markers was successfully used to genotype 753 individuals from 43 populations in five Tropical West and Central African Countries. These loci have an expected heterozygosity range of 0.007–0.501 and F
ST
from 0 to 0.306.
TL;DR: It is demonstrated that COI barcoding is a suitable tool in identifying illegally imported A. anguilla, which can support enforcement and prosecution as well as enable international cooperation between Europe and Asia.
Abstract: Eel farming in Asia relies on wild-caught juvenile “glass eels” of the genus Anguilla. When supplies of Japanese eels (Anguilla japonica) declined in the 1990s, Asian eel farming shifted to using European eels (Anguilla anguilla). The European eel is currently classified as “Critically Endangered”, and export out of Europe has been suspended since March 2009. In early 2016, glass eels were seized at the Hong Kong International Airport and genetically identified using the COI barcode region. Samples matched A. anguilla with a similarity range of 99.39–99.85 %. To our knowledge, this is the first documented case of illegal trade of A. anguilla from Europe into Hong Kong using genetic evidence. Furthermore, multiple isolated incidents of eel seizures by customs indicate that Hong Kong is a major hub facilitating illegal trade in eels from Europe to Asia. We demonstrated that COI barcoding is a suitable tool in identifying illegally imported A. anguilla, which can support enforcement and prosecution as well as enable international cooperation between Europe and Asia.
TL;DR: The phylogenetic analysis suggested that the sampled Acer species formed a monophyletic clade, and the cpDNA of A. davidii is closely related to that of congeneric A. morrisonense.
Abstract: The whole chloroplast genome (cp DNA) sequence of Acer davidii Franch has been characterized from Illumina pair-end sequencing. The complete cpDNA was 157,044 bp in length, containing a large single copy region (LSC) of 85,410 bp and a small single copy region (SSC) of 18,112 bp, which were separated by a pair of 26,761 bp inverted repeat regions (IRs). The cpDNA contained 134 genes, including 86 protein-coding genes (78 PCG species), forty tRNA genes (31 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 21 gene species occur in double copies. The overall AT content of A. davidii cpDNA is 62.1 %, while the corresponding values of the LSC, SSC and IR regions are 63.9, 67.7 and 57.3 %, respectively. The phylogenetic analysis suggested that the sampled Acer species formed a monophyletic clade, and the cpDNA of A. davidii is closely related to that of congeneric A. morrisonense.
TL;DR: Phylogenetic analysis indicated that R. speculum is closely related to Ricania marginalis, a major agricultural pest for a variety of crops in tropical and subtropical areas.
Abstract: The Asian planthopper Ricania speculum is a major agricultural pest for a variety of crops in tropical and subtropical areas. Rapid species diagnosis and source determination of this pest would be essential to the formulation of effective management, control and prevention strategy, and mitochondrial DNA has proven powerful for such purposes. In this study, we assembled and characterized its complete mitochondrial genome from Illumina sequencing reads. The whole genome of R. speculum is 15,729 bp in length, and encodes the typical set of 37 mitochondrial genes (incl. 13 PCGs, 22tRNAs and 2 rRNAs) and a control region. All PCGs are initiated with the typical ATN codons, and are terminated with either the complete TAA/TAG codons or the incomplete T(aa) codon. The nucleotide composition is asymmetric (47.4 %A, 14.8 %C, 9.5 %G and 28.3 %T) with an obvious bias towards A and T. Phylogenetic analysis indicated that R. speculum is closely related to Ricania marginalis.
TL;DR: Phylogenetic analysis indicates that A. miaotaiense is closely related to the congeneric A. morrisonense and A. buergerianum, and strongly supports that Acer and Dipteronia are sister taxa.
Abstract: Acer miaotaiense (Sapindales: Aceraceae) is a rare and vulnerable tree species endemic to China’s Mts. Qinling and Mts. Bashan. In this study, its complete chloroplast genome was assembled and characterized from the high-throughput Illumina sequencing data. The circular genome is 156,595 bp long, and contains a pair of inverted repeat (IR) regions of 26,100 bp each, separated by a large single-copy (LSC) region of 86,327 bp and a small single-copy (SSC) region of 18,068 bp. It harbors 137 genes, including 89 protein-coding genes (80 PCG species), 40 tRNA genes (30 tRNA species) and eight rRNA genes (four rRNA species). Its nucleotide composition is asymmetric (30.69 % A, 19.32 % C, 18.57 % G & 31.42 % T) with an overall A+T content of 62.12 %. Phylogenetic analysis indicates that A. miaotaiense is closely related to the congeneric A. morrisonense and A. buergerianum, and strongly supports that Acer and Dipteronia are sister taxa.
TL;DR: The data suggest cartilaginous species (sharks, rays, and skates) constitute an important part of the New Zealand fur seal diet, and some qualitative food competition between New Zealandfur seals and commercial fisheries in exploiting marine species is indicated.
Abstract: The New Zealand fur seal (Arctocephalus forsteri) is one of many pinniped species that has shown a remarkable recovery from the brink of extinction after cessation of commercial sealing during the eighteenth and nineteenth centuries. It is commonly believed that this species competes with recreational and commercial fisheries. We identified prey items using massive parallel sequencing from New Zealand fur seal faecal samples that were collected throughout the species distribution. The data support generalist feeding behaviour for this species. The diet composition showed significant geographical and inter-seasonal variation. As many as 46 species of fish and 18 species of cephalopod were identified from a single colony. The data suggest cartilaginous species (sharks, rays, and skates) constitute an important part of the New Zealand fur seal diet. Approximately 10 % of the species identified in the seal diet were of significant commercial value, which indicates some qualitative food competition between New Zealand fur seals and commercial fisheries in exploiting marine species.
TL;DR: A species-specific assay for detection of North American river otters using eDNA was developed and tested for specificity against closely-related mustelids native to western North America, and was validated through testing environmental samples.
Abstract: Environmental DNA (eDNA) is an effective tool for the detection of elusive or low-density aquatic organisms. However, it has infrequently been applied to mammalian species. North American river otters (Lontra canadensis) are both broad ranging and semi-aquatic, making them an ideal candidate for examining the uses of eDNA for detection of mammals. We developed a species-specific assay for detection of North American river otters using eDNA. The assay was tested for specificity against closely-related mustelids native to western North America, and was validated through testing environmental samples.
TL;DR: The dietary composition were analyzed in 23 samples of finless porpoise collected across its distributing range and revealed more 9 taxa than morphological traits, which is crucial in conservation of the species.
Abstract: Knowledge of the dietary choices of organisms is the key to understanding their roles in ecosystems, which plays an important role in conservation of species that are vulnerable to overexploitation. Finless porpoise Neophocaena asiaeorientalis sunameri is one of the most endangered marine mammalian. In this study, the dietary composition were analyzed in 23 samples of finless porpoise collected across its distributing range. The prey species was identified using morphological and mitochondrial COI barcoding analyses. A total of 21 species including 16 fish, 2 cephalopods, 2 crustaceans, and one bivalve were identified based on both two methods. However, mtDNA barcoding increased taxonomic resolution and revealed more 9 taxa than morphological traits. For the quantitative analysis of the dietary, Odontamblyopus lacepedii, Scomber australasicus, Larimichthys polyactis, Nibea albiflora and Saurida elongate were dominant. Moreover, geographical variation in prey composition was observed comparing with previous studies. Our reports offered important information in understanding biological habits of finless porpoise which is crucial in conservation of the species.
TL;DR: This investigation implemented a GBS protocol and different bioinformatics tools to identify a novel SNP panel and investigate the genetic structure and variability in populations of little owl sampled from seven geographical regions in Europe.
Abstract: Single nucleotide polymorphisms (SNPs) are becoming the most utilized markers in population genetics studies. Reduced representation genome techniques, as genotyping-by-sequencing (GBS), allow identifying great numbers of polymorphisms that are useful to analyze genetic diversity in non-model organisms. In this investigation, we implemented a GBS protocol and different bioinformatics tools to identify a novel SNP panel and investigate the genetic structure and variability in populations of little owl (Athene noctua) sampled from seven geographical regions in Europe (Balkans, north-west Europe, north, central and south Italy, Spain and Portugal). We obtained a total of 22,185 putative SNPs and 1306 indels. After the filtering procedure, 7175 SNP loci and 53 individuals met the stringent quality control measures. Neutrality test identified 281 candidate loci under positive selection, which were used for population genetic analyses. The selected SNP panel allowed an accurate description of the genetic structure of the little owl.
TL;DR: 100 SNP and one Indel markers were developed for Khaya using a combination of restriction associated DNA sequencing and low coverage MiSeq genome sequencing and successfully used to genotype a set of 1919 individuals, representing 5 Khaya species from 18 African countries, using MassARRAY®iPLEX™ genotyping.
Abstract: 100 SNP and one Indel markers were developed for Khaya using a combination of restriction associated DNA sequencing and low coverage MiSeq genome sequencing. The marker set was successfully used to genotype a set of 1919 individuals, representing 5 Khaya species from 18 African countries, using MassARRAY®iPLEX™ genotyping.
TL;DR: It is concluded that DNA barcoding can improve the identification of salvaged bat carcasses especially when rare and uncommon species are encountered and has other practical applications, such as identifying remains from hibernacula or identifying species from fecal samples at roost sites or other locales.
Abstract: Bat fatality monitoring at wind turbines depends upon reliable identification of carcasses. Using reference mitochondrial cytochrome c oxidase I gene sequences mined from GENBANK and new sequences from collected samples, we constructed maximum likelihood trees including all 47 bat species found in the USA and tested the use of this locus for DNA barcoding these bat species. In this study, 80 % of species examined had distinct barcodes, including species currently listed as threatened or endangered. Nine of 17 Myotis bat species examined did not form distinct clades and had very low inter-specific genetic distances (1.4 %), thereby making this barcoding technique unreliable for some members of this genus. We then applied this technique to DNA samples from 892 bats salvaged from wind farms across four states. Using DNA barcoding, we were able to identify 14 carcasses to species that could not be identified in the field due to extensive decomposition and scavenging, and determined that another 18 carcasses had been misidentified in the field. Furthermore, we found field misidentifications increased with time until discovery. We conclude that DNA barcoding can improve the identification of salvaged bat carcasses especially when rare and uncommon species are encountered. This technique has other practical applications, such as identifying remains from hibernacula (potentially including carcasses of unknown bats with white-nose syndrome) or identifying species from fecal samples at roost sites or other locales.
TL;DR: Phylogenetic analysis corroborated the traditional morphological taxonomy of the family Rosaceae, and indicated that M. prunifolia was phylogenetically closely related to the genus Pyrus.
Abstract: Malus prunifolia is a species of crabapple tree with high ecological and economic values. In this study, we assembled its complete chloroplast genome from high-throughput sequencing data. The circular double-stranded genome is 160,041 bp in length, and exhibits a typical quadripartite structure of the large (LSC, 88,119 bp) and small (SSC, 19,204 bp) single-copy regions, separated by a pair of inverted repeat regions (IRs, 26,359 bp each). It contains 129 genes, including 84 protein-coding genes (77 PCG species), 37 transfer RNA genes (30 tRNA species) and eight ribosomal RNA genes (four rRNA species). The nucleotide composition is asymmetric (31.32 % A, 18.64 % C, 17.92 % G & 32.12 % T) with an overall A+T content of 63.44 %. Phylogenetic analysis corroborated the traditional morphological taxonomy of the family Rosaceae, and indicated that M. prunifolia was phylogenetically closely related to the genus Pyrus.
TL;DR: The chloroplast genome of a Chinese tulip tree, L. chinense, contained the conservative quadripartite structure present in most Magnoliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs.
Abstract: Liriodendron chinense is a rare Tertiary relict tree species. In this study, we report the complete chloroplast genome of a Chinese tulip tree, L. chinense. The total genome size was 159,429 bp in length, containing a pair of inverted repeats (IRs) of 26,333 bp, separated by large single copy (LSC) and small single copy (SSC) of 87,766 and 18,997 bp, respectively. The chloroplast genome contained the conservative quadripartite structure present in most Magnoliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs. Among these genes, 15 harbored a single intron, and 2 contained a couple of introns. The overall G+C content of the cpDNA is 39.2 %, while the corresponding values of the LSC, SSC and IR regions are 37.8, 34.3 and 43.2 % respectively. A maximum likelihood phylogenomic analysis showed that L. chinense is closely related to L. tulipifera that belongs to the tribe Magnoliaceae.
TL;DR: The chloroplast genome contains the conservative structure present in most Liliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs, and 15 harbor a single intron, and 2 contain a couple of introns.
Abstract: Lilium cernuum is endangered and was listed in the category of key protected wild plants in China. In this study, we report the complete chloroplast genome of L. cernuum using Illumina paired-end sequencing. The entire chloroplast genome maps as a circular molecule of 152,604 bp built with a quadripartite organization: two inverted repeats (IRs) of 26,481 bp separated by a large single copy (LSC) sequence of 82,058 bp and a small single copy (SSC) sequence of 17,584 bp. The chloroplast genome contains the conservative structure present in most Liliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs. Among these genes, 15 harbor a single intron, and 2 contain a couple of introns. A maximum likelihood phylogenomic analysis showed that L. cernuum was closely related to L. tsingtauense and L. hansonii that belonged to the family Liliaceae.
TL;DR: This study used Illumina Hiseq2500 sequencing to develop single nucleotide polymorphism (SNP) markers in S. prenanti and these SNP markers should not only be useful for population conversation, but also for construction of genetic linkage map and economic performance improvement of S.Prenanti.
Abstract: Schizothorax prenanti (S. prenanti), one of the important endemic commercial fish in China, is mainly distributing in the upstream of the River Yangtze and the tributaries. The wild population is facing serious challenges of germplasm degeneration due to the overfishing, water pollution and construction of hydropower stations; therefore, it is very urgent to develop genetic resource of S. prenanti to protect the wild population. In this study, we used Illumina Hiseq2500 sequencing to develop single nucleotide polymorphism (SNP) markers in S. prenanti. From 37,785 unigenes with functional annotation, 857,535 putative SNPs were identified. Among them, 33 SNPs from immune-related genes were randomly selected and 20 loci exhibited significant polymorphisms in genotyping by Sequenom MassARRAY. As far as our best knowledge, this is the first report about the SNP markers development in S. prenanti based on Illumina RNA sequencing. These SNP markers should not only be useful for population conversation, but also for construction of genetic linkage map and economic performance improvement of S. prenanti.
TL;DR: The maximum likelihood phylogenetic analysis based on 15 chloroplast genomes revealed that P. veris was closely related to that of congeneric P. sinensis.
Abstract: Primula veris is an important spring blooming perennial with high ecological and genetic values. In the present study, the complete chloroplast (cp) genome of Primula veris (Primulaceae) was assembled based on the Illumina sequencing reads. The complete chloroplast genome of P. veris was 150,856 bp in length and contained a pair of IR regions (25,524 bp) separated by a small single copy region (17,760 bp) and a large single copy region (82,048 bp). The cp genome of P. veris encoded 131 genes including 86 protein-coding genes (79 PCG species), 37 tRNA genes (29 tRNA species) and eight ribosomal RNA genes (four rRNA species). The overall AT content of P. veris cp genome is 62.9 %. The maximum likelihood phylogenetic analysis based on 15 chloroplast genomes revealed that P. veris was closely related to that of congeneric P. sinensis.
TL;DR: This research provides an efficient and accurate method for the genetic monitoring of the restocking program, but also for others aspects of conservation, including genetic diversity evaluation, effective population size estimation, and inbreeding assessment.
Abstract: The only remaining population of the critically endangered European sturgeon, Acipenser sturio, is located in the Gironde basin (France). A restoration program initiated 20 years ago has allowed more than one and a half million individuals to be stocked. Effective monitoring of this population is a key prerequisite in ensuring the sustainability of this species in the wild. We report the development of a novel microsatellite multiplex assay for genetic monitoring of A. sturio. Diversity of a set of 18 loci was low to moderate, with a number of alleles and observed heterozygosity ranging from 4 to 7 and 0.33 to 0.74 respectively, depending on markers. A set of captive-born progeny of known relatives (n = 72) was used to examine the efficiency of this assay in assigning parentage to offspring. Three different programs were used. Correct assignment success was generally high (above 90 %), but differed between programs. Parentage analysis of individuals captured in the Gironde estuary (n = 193) demonstrated that most offspring (91.2 %) are unambiguously allocated to parent pairs from the broodstock. Our research provides an efficient and accurate method for the genetic monitoring of the restocking program, but also for others aspects of conservation, including genetic diversity evaluation, effective population size estimation, and inbreeding assessment.