Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment

Zhang, Min; Wei, Min; Dong, Zhiguo; Duan, Haibao; Mao, Shuang; Feng, Senlei; Li, Wenqian; Sun, Zepeng; Li, Jiawei; Yan, Kanglu; Líu, Hao; Meng, Xianhong; Ge, Hongxing

doi:10.1186/s12896-019-0595-6

Cited by 6 publications

(5 citation statements)

References 46 publications

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“…Furthermore, fecal samples generally have lower DNA concentrations compared to other sample types, such as blood or tissue. The presence of polymerase chain reaction inhibitors in feces can also interfere with DNA amplification, limiting the reliability and sensitivity of sex determination assays or introducing variability in marker sequences [ 57 , 58 , 59 ]. According to previous estimates, the cost of DNA testing for sex determination is approximately USD 1 per sample, excluding labor costs and only considering the expenses for reagents and plates [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

Predicting Sex in White Rhinoceroses: A Statistical Model for Conservation Management

Martínez

Andrés

Caperos

et al. 2023

Animals

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Ensuring the effective management of every rhinoceros population is crucial for securing a future for the species, especially considering the escalating global threat of poaching and the challenges faced in captive breeding programs for this endangered species. Steroid hormones play pivotal roles in regulating diverse biological processes, making fecal hormonal determinations a valuable non-invasive tool for monitoring adrenal and gonadal endocrinologies and assessing reproductive status, particularly in endangered species. The purpose of this study was to develop a statistical model for predicting the sex of white rhinoceroses using hormonal determinations obtained from a single fecal sample. To achieve this, 562 fecal samples from 15 individuals of the Ceratotherium simum species were collected, and enzyme immunoassays were conducted to determine the concentrations of fecal cortisol, progesterone, estrone, and testosterone metabolites. The biological validation of the method provided an impressive accuracy rate of nearly 80% in predicting the sex of hypothetically unknown white rhinoceroses. Implementing this statistical model for sex identification in white rhinoceroses would yield significant benefits, including a better understanding of the structure and dynamics of wild populations. Additionally, it would enhance conservation management efforts aimed at protecting this endangered species. By utilizing this innovative approach, we can contribute to the preservation and long-term survival of white rhinoceros populations.

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Section: Discussionmentioning

confidence: 99%

Predicting Sex in White Rhinoceroses: A Statistical Model for Conservation Management

Martínez

Andrés

Caperos

et al. 2023

Animals

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“…Total DNA was extracted with the sodium dodecyl sulphate (SDS) phenol-chloroform method and according to the detailed protocol for the DNA extraction as previously described by Li et al (2020). The PCR system and program in this study was done as previously described by Zhang et al (2019). Specifically, the used PCR system consisted of 1 µl of template DNA (about 30 ng), 2 µl of primer mix, 1 µl of universal fluorescent primers, 10 µl of 2 × Taq PCR Master Mix (TaKaRa, Dalian, China), and 6 µl of ddH 2 O to form a total volume of 20 µl.…”

Section: Methodsmentioning

confidence: 99%

SSR Marker-Based Genetic Resource Assessment of the Rainbow Clam Moerella iridescens Along the Coasts of China: Implications for Strategy of Conservation Management

Li¹,

Gao²,

Zhao³

et al. 2022

Front. Mar. Sci.

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This study aims to determine the genetic structure of rainbow clam Moerella iridescens in different sea areas of China. Seventeen pairs of microsatellite primers (SSR) were used to amplify the SSRs of rainbow clam in Lianyungang of Haizhou Bay, Chongming of Shanghai, Ningde of Fujian, Daishan of Zhoushan, and Cixi and Wenzhou of Zhejiang. A total of 1,146 alleles were detected in 310 individuals from the 17 SSR loci. The average observed heterozygosity of six populations was 0.4381−0.6139, the average expected heterozygosity was 0.5897−0.7325, and the average Shannon diversity index was 1.2655−1.7998. The clams exhibited rich genetic diversity, and the FST of the genetic differentiation index of the six populations was 0.0470, indicating low genetic differentiation among the populations. The results indicated that rainbow clams along the coasts of China exhibited high diversity and low population differentiation.

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“…The use of faecal DNA for genetic studies of marine species is even more restricted due to degradation and contamination in seawater [ 11 ]. Furthermore, the age of faecal samples may impact retrieval of target DNA, i.e., higher yield and quality of target DNA may be extracted from fresh compared to old scats [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…Depending on the application, a more affordable DNA extraction method, if available, may also be more practical when a large number of samples needs to be processed. Amongst the different DNA extraction techniques available, some of the most widely used include the QIAamp Fast DNA Stool Mini Kit (hereafter referred to as QIAamp) [ 8 , 16 ], phenol-chloroform-isoamyl alcohol (PCI) [ 12 , 17 ], and cetyltrimethyl ammonium bromide (CTAB) [ 18 ]. The 2CTAB/PCI protocol, a combination of the latter two procedures, is a particularly notable extraction technique as it has demonstrated success in extracting DNA from herbivore faeces [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong

Ooi¹,

McMichael²,

Hunter³

et al. 2023

PLoS ONE

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Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new ‘High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol’ (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.

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Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment

Cited by 6 publications

References 46 publications

Predicting Sex in White Rhinoceroses: A Statistical Model for Conservation Management

Predicting Sex in White Rhinoceroses: A Statistical Model for Conservation Management

SSR Marker-Based Genetic Resource Assessment of the Rainbow Clam Moerella iridescens Along the Coasts of China: Implications for Strategy of Conservation Management

A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong

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