A comparison of next-generation sequencing with clone sequencing in the diet analysis of Asian great bustard

Gong, Minghao; Ning, Yu; Han, Morigen; Zhao, Chenyang; Tian, Jingxing; Li, Linwei; Xiao, Hongye; Liu, Gang

doi:10.1007/s12686-017-0952-5

Cited by 8 publications

(9 citation statements)

References 19 publications

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“…Diet analysis are important for understanding how animal populations respond to resource distribution and variety as well as how to manage them (Gordon et al., 2019). Dietary information has been used in addition to pure feeding ecology in a variety of applied studies (Gong et al., 2017). Accurate identification of foods is a prerequisite to fully understanding the feeding ecology of a species and effectively controlling pest numbers (Heroldova et al., 2008).…”

Section: Introductionmentioning

confidence: 99%

“…For natural populations, it is difficult to accurately and efficiently assess wildlife diets, because of their elusive predatory behaviors and versatile feeding habits (Gong et al., 2017; Ozaki et al., 2018). Identifying food items with the highest taxonomic resolution is nearly impossible with traditional microhistological analysis of gut contents and stable isotope analysis (Jeunen et al., 2019; Murray et al., 2016; Rytkonen et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

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DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts

Tang

Xie

Liu

et al. 2020

Ecology and Evolution

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts

Tang

Xie

Liu

et al. 2020

Ecology and Evolution

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“…Diet analysis are important for understanding how animal populations respond to resource distribution and variety as well as how to manage them (Gordon et al 2019). Dietary information has been used in addition to pure feeding ecology in a variety of applied studies (Gong et al 2017). Accurate identification of foods is a prerequisite to fully understanding the feeding ecology of a species and effectively controlling pest numbers (Heroldova et al 2008).…”

Section: Introductionmentioning

confidence: 99%

DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts

Tang¹,

Xie²,

Liu³

et al. 2020

Preprint

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Diet analysis of potential small mammals pest species is important for understanding feeding ecology and evaluating their impact on crops and stored foods. Chinese mole shrew (Anourosorex squamipes), distributed in Southwest China, has previously been reported as a farmland pest. Effective population management of this species requires a better understanding of its diet, which can be difficult to determine with high taxonomic resolution using conventional microhistological methods. In this study, we used two DNA metabarcoding assays to identify 38 animal species and 65 plant genera from shrew stomach contents, which suggest that A. squamipes is an omnivorous generalist. Earthworms are the most prevalent (>90%) and abundant (>80%) food items in the diverse diet of A. squamipes. Species of the Fabaceae (frequency of occurrence [FO]: 88%; such as peanuts) and Poaceae (FO: 71%; such as rice) families were the most common plant foods identified in the diet of A. squamipes. Additionally, we found a seasonal decrease in the diversity and abundance of invertebrate foods from spring and summer to winter. Chinese mole shrew has a diverse and flexible diet throughout the year to adapt to seasonal variations in food availability, contributing to its survival even when food resources are limited. This study provides a higher resolution identification of the diet of A. squamipes than has been previously described and is valuable for understanding shrew feeding ecology as well as evaluating possible species impacts on crops.

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“…It can perform parallel detection of enormous DNA molecules in one reaction without the complicated cloning procedures. In comparison with CBS, NGS can detect a low‐frequency mutation <1%, with a higher sensitivity than CBS . Although NGS can provide a large amount of data, subsequent analysis encounters great challenges, such as requiring advanced computers and specialized bioinformatics software that must be operated by professionals.…”

Section: Introductionmentioning

confidence: 99%

“…In many previous studies, CBS and Roche 454FLX(UDPS) were used to detect HBV quasispecies, which focused on the HBV RT region, 10,14,15 pre-C/core region, [16][17][18][19] pre S/S region 20,21 or fulllength sequence. [22][23][24][25][26] The comparison between NGS technology based on the Illumina Miseq platform and CBS to describe the difference of heterogeneity of the HBV X-region quasispecies has not been reported.…”

Section: Introductionmentioning

confidence: 99%

Analysis of HBV X gene quasispecies characteristics by next‐generation sequencing and cloning‐based sequencing and its association with hepatocellular carcinoma progression

Mei

Ren

Long³

et al. 2019

Journal of Medical Virology

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Objectives This study aimed to describe the differences between next‐generation sequencing (NGS) and cloning‐based sequencing (CBS) in HBX quasispecies research and primitively investigate the relationship between the dominant HBX quasispecies and hepatocellular carcinoma (HCC). Methods A total of 12 serum samples were collected. Serum hepatitis B virus (HBV) DNA was extracted, and the HBV X‐region (HBX) was amplified by nested polymerase chain reaction (PCR). The PCR products were simultaneously tested with NGS and CBS to detect quasispecies of the HBX. Results A total of 9348 eligible quasispecies sequences were obtained by NGS, which were much larger than the 98 of that by CBS. By the phylogenetic tree, the dominant quasispecies sequence of each sample could be found, although they had several nucleotides differences between the dominant quasispecies sequences found by CBS and NGS. By comparing the quasispecies heterogeneity, it was found that the quasispecies complexity value of HBV X‐region obtained by NGS was higher than CBS (P < 0.05). The diversity values, including d, dS, dN, an d d N/ dS obtained by NGS were lower than by CBS (all of P < 0.01). The relativity of Spearman(rs) in d, dS, and dN were statistically significant (rs_ d = 0.865, P = 0.001; rs_ dS = 0.722, P = 0.014; and rs_ dN = 0.738, P = 0.011, respectively). There were 21 different bases between the HBX quasispecies of case A and control B. Conclusion The results of this can be used as guidance when researchers plan to choose a suitable method to study quasispecies, especially the HBV X gene quasispecies. Some high‐risk mutations of HBX quasispecies were also found in this study and their relationship with HCC need deeper exploration.

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A comparison of next-generation sequencing with clone sequencing in the diet analysis of Asian great bustard

Cited by 8 publications

References 19 publications

DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts

DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts

DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts

Analysis of HBV X gene quasispecies characteristics by next‐generation sequencing and cloning‐based sequencing and its association with hepatocellular carcinoma progression

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