Evaluation of the 5′ end of the 16S rRNA gene as a DNA barcode marker for the Cephalopoda

Sánchez, Gustavo; Tomano, Satoshi; Umino, Tetsuya; Wakabayashi, T.; Sakai, Mitsuo

doi:10.1007/s12562-015-0962-8

Cited by 11 publications

(10 citation statements)

References 40 publications

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“…2A, D), which are concordant with the two cluster patterns recognized in this study based on the general trends of ontogenetic trajectories of septal spacing. Based on this concordance in plural phylogenetic trees among eight literatures (Bonnaud et al 2006; Yoshida et al 2006, 2010; Anderson et al 2011; Dai et al 2012; Lindgren et al 2012; Sanchez et al 2016; Lü et al 2019), therefore, we hypothesized that the ontogenetic trajectories of septal spacing among modern cuttlefishes are phylogenetically dependent. However, several phylogenetic trees are not all concordant with the two cluster patterns based on the general trends of ontogenetic trajectories of septal spacing (Fig.…”

Section: Discussionmentioning

confidence: 76%

“…The phylogenetic affinity of modern sepiids (including the five examined species) has been estimated based on DNA analyses (Bonnaud et al 2006; Yoshida et al 2006, 2010; Anderson et al 2011; Dai et al 2012; Lindgren et al 2012; Sanchez et al 2016; Lü et al 2019). However, the phylogeny of the five examined species has been still controversial, and therefore, a consensus of the phylogeny of the five examined species is not obtained (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Supposed phylogeny of the five examined species based on DNA molecular analyses. A, Bonnaud et al (2006); B, Yoshida et al (2006); C, Yoshida et al (2010); D, Anderson et al (2011); E, Lindgren et al (2012); F, Dai et al (2012); G, Sanchez et al (2016). All phylogenetic trees are simplified from the originals, showing the relationship among only the five examined species.…”

Section: Methodsmentioning

confidence: 99%

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Ontogenetic trajectories of septal spacing in modern cuttlefishes are phylogenetically dependent

Noba

Yasumuro

Ikeda

et al. 2020

LET

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In this study, the ontogenetic trajectories of septal spacing between succeeding chambers of five modern cuttlefishes, Sepia esculenta, S. lycidas, S. latimanus, S. pharaonic and Sepiella japonica, which were all wild‐caught around Japan, were analysed. The ontogenetic trajectories of septal spacing of all examined cuttlefishes demonstrate a decrease in septal spacing followed by an increase during the earliest ontogenetic stage. This trend is assumed to be related to hatching. After the rapid decrease and increase in septal spacing, species‐dependent trends occur irrespective of sex and locality. Based on cluster analyses of general trends recognized in each species, the five examined species can be categorized into two groups: (1) a group by S. pharaonis, S. esculenta and Sepiella japonica; and (2) S. latimanus and S. lycidas as more distant branching groups within the five examined species. This classification is concordant with some phylogenetic clades determined from DNA analyses. Therefore, we hypothesized that the ontogenetic trajectories of septal spacing among modern cuttlefishes are phylogenetically dependent. If this hypothesis holds in fossil cuttlefishes, the examination of ontogenetic trajectories of septal spacing would give new insight into the recognition not only of the life history but also of the phylogeny of fossil cuttlefishes.

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Section: Discussionmentioning

confidence: 76%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Ontogenetic trajectories of septal spacing in modern cuttlefishes are phylogenetically dependent

Noba

Yasumuro

Ikeda

et al. 2020

LET

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“…DNA testing of cephalopod food products and ingredients is an effective strategy to identify and authenticate species, detect contaminants or adulterants, and verify label claims. This strategy can also support traceability regulations and prevent food fraud and health problems . Previous studies have reported over 20% of ambiguity and attempts to mislead consumers by using incorrect labels when buying products labeled with the commercial name Galician octopus, which is used to legally protect this high value‐added product in national and international markets .…”

Section: Introductionmentioning

confidence: 99%

Lab experience with seafood control at the undergraduate level: Cephalopods as a case study

Fernández

Rodrı́guez-Muñiz

Molina

et al. 2020

Biochem Molecular Bio Educ

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The correct labeling of seafood is important to protect nature and the rights of consumers. Given the certainty that the resources of the sea are not inexhaustible, only strict regulations and the implementation of sustainable fishing systems and reliable and traceable marketing systems can help ensure the long-term sustainability of fishery resources. Detecting mislabeling and seafood fraud is a useful resource for improving students' motivation and developing active learning methodologies in higher education. In the present study, we have proposed to the students a lab exercise consisting of exploring 25 different commercial cephalopod products from three major European supermarkets by using DNA barcoding and analyzing the results under the framework of EU and Spanish regulations. The problem is connected with the last theme (traceability) of the Conservation Genetics and Breeding course with the aim of providing students with a practical research lab experience about a real problem before going deeper into more theoretical contents. In this way, they can use the knowledge and the skills they acquired previously to better comprehend and think critically about the problem.Findings from students' answers to a survey revealed that the use of this approach generates useful information for communities, increases curiosity and feelings of benefit, and leads to high levels of satisfaction with lab practices compared with those in other courses. In conclusion, lab exercises focused on seafood control, in addition to being viable, can be used as a tool in classes to improve students' commitment to higher education. K E Y W O R D Sbarcoding, cephalopods, lab experiences, seafood control, university

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“…In a preliminary study conducted on Chlorella sorokiniana NS5, we found that high molecular weight DNA with good integrity could only be obtained using the TNES-urea buffer. This buffer is commonly used for preservation and DNA extraction from fish, mollusk and animal tissue [8,9]. We shortly discovered that excluding 2-ME from the standard SDS/CTAB lysis buffer yielded DNA of good integrity from C. sorokiniana.…”

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confidence: 99%

Inclusion of 2-Mercaptoethanol in Lysis Buffer Could Interfere with Isolation of High Molecular Weight DNA from Freshwater Microalgae

2017

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2-mercaptoethanol (2-ME), alongside polyvinylpyrrolidone is commonly used in plant DNA extractions to deal with polyphenols, which could interfere with extraction and downstream applications. 2-ME is also commonly used to denature proteins and nucleases, especially RNAses. On the contrary, we found that the presence of 2-ME in lysis buffer interfered with DNA extraction from 12 strains of freshwater microalgae, resulting in DNA with poor integrity. We also found that the TNES-urea buffer, commonly used for preservation and DNA extraction from fish, appears as effective as the SDS and CTAB buffer for some microalgae strains. Results from our study suggests that the inclusion of 2-ME in DNA extraction protocols may be detrimental for isolation of good quality DNA from freshwater microalgae, and therefore recommend eliminating it or testing varying concentrations of 2-ME when developing species-specific extraction protocols for microalgae.

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Evaluation of the 5′ end of the 16S rRNA gene as a DNA barcode marker for the Cephalopoda

Cited by 11 publications

References 40 publications

Ontogenetic trajectories of septal spacing in modern cuttlefishes are phylogenetically dependent

Ontogenetic trajectories of septal spacing in modern cuttlefishes are phylogenetically dependent

Lab experience with seafood control at the undergraduate level: Cephalopods as a case study

Inclusion of 2-Mercaptoethanol in Lysis Buffer Could Interfere with Isolation of High Molecular Weight DNA from Freshwater Microalgae

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