Assessment of the Food Habits of the Moroccan Dorcas Gazelle in M’Sabih Talaa, West Central Morocco, Using the trnL Approach

Baamrane, Moulay Abdeljalil Ait; Shehzad, Wasim; Ouhammou, Ahmed; Abbad, Abdelaziz; Naïmi, Mohamed; Coissac, Éric; Taberlet, Pierre; Znari, Mohammed

doi:10.1371/journal.pone.0035643

Cited by 64 publications

(68 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…) and the P6 loop of the plastid DNA trnL intron (Baamrane et al . ), all of which are typically <100 bp. The preference for a short, non‐standard DNA marker lies in its improved primer universality (Coissac, Riaz & Puillandre ) and the fact that these markers can be easily sequenced using current Illumina technology.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

Liu

et al. 2013

Methods Ecol Evol

View full text Add to dashboard Cite

Summary1. Metabarcoding of mixed arthropod samples for biodiversity assessment has mostly been carried out on the 454 GS FLX sequencer (Roche, Branford, Connecticut, USA), due to its ability to produce long reads (≥400 bp) that are believed to allow higher taxonomic resolution. The Illumina sequencing platforms, with their much higher throughputs, could potentially reduce sequencing costs and improve sequence quality, but the associated shorter read length (typically <150 bp) has deterred their usage in next-generation-sequencing (NGS)-based analyses of eukaryotic biodiversity, which often utilize standard barcode markers (e.g. COI, rbcL, matK, ITS) that are hundreds of nucleotides long. 2. We present a new Illumina-based pipeline to recover full-length COI barcodes from mixed arthropod samples. Our new assembly program, SOAPBarcode, a variant of the genome assembly program SOAPdenovo, uses paired-end reads of the standard COI barcode region as anchors to extract the correct pathways (sequences) out of otherwise chaotic 'de Bruijn graphs', which are caused by the presence of large numbers of COI homologs of high sequence similarity. 3. Two bulk insect samples of known species composition have been analysed in a recently published 454 metabarcoding study (Yu et al. 2012) and are re-analysed by our analysis pipeline. Compared to the results of Roche 454 (c. 400-bp reads), our pipeline recovered full-length COI barcodes (658 bp) and 17-31% more species-level operational taxonomic units (OTUs) from bulk insect samples, with fewer untraceable (novel) OTUs. On the other hand, our PCR-based pipeline also revealed higher rates of contamination across samples, due to the Illumina's increased sequencing depth. On balance, the assembled full-length barcodes and increased OTU recovery rates resulted in more resolved taxonomic assignments and more accurate beta diversity estimation. 4. The HiSeq 2000 and the SOAPBarcode pipeline together can achieve more accurate biodiversity assessment at a much reduced sequencing cost in metabarcoding analyses. However, greater precaution is needed to prevent cross-sample contamination during field preparation and laboratory operation because of greater ability to detect non-target DNA amplicons present in low-copy numbers.

show abstract

Section: Discussionmentioning

confidence: 99%

“…For instance, there have been diet analysis of herbivores (Baamrane et al . ) and carnivores (Shehzad et al . ,b) via faecal samples, and similar strategies have been applied on soil samples (Bienert et al .…”

Section: Discussionmentioning

confidence: 99%

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

Liu

et al. 2013

Methods Ecol Evol

View full text Add to dashboard Cite

show abstract

“…The amplification of the P6 loop of the chloroplast trnL (UAA) intron was carried out using primers g and h (Taberlet et al, 2007; Table 2). Two other sets of primer pairs were used to amplify a portion of the first internal transcribed spacer (ITS1) of nuclear ribosomal DNA of the families Asteraceae (primers ITS1-F and ITS1Ast-R) and Poaceae (primers ITS1-F and ITS1Poa-R; Table 2; Baamrane et al, 2012). The primer pair 16SMAV-F and 16SMAV-R (Table 2; De Barba et al, 2014) was also applied to amplify a fragment of the 16S rDNA mitochondrial gene of mollusks, arthropods and vertebrates.…”

Section: Laboratory Proceduresmentioning

confidence: 99%

DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents

et al. 2015

View full text Add to dashboard Cite

Closely related sympatric species commonly develop different ecological strategies to avoid competition. Ctenomys minutus and C. flamarioni are subterranean rodents parapatrically distributed in the southern Brazilian coastal plain, showing a narrow sympatric zone. To gain understanding on food preferences and possible competition for food resources, we evaluated their diet composition performing DNA metabarcoding analyzes of 67 C. minutus and 100 C. flamarioni scat samples, collected along the species geographical ranges. Thirteen plant families, mainly represented by Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet of C. minutus. For C. flamarioni, 10 families were recovered, with a predominance of Poaceae, Araliaceae and Asteraceae. A significant correlation between diet composition and geographical distance was detected in C. minutus, whereas the diet of C. flamarioni was quite homogeneous throughout its geographical distribution. No significant differences were observed between males and females of each species. However, differences in diet composition between species were evident according to multivariate analysis. Our results suggest some level of diet partitioning between C. flamarioni and C. minutus in the sympatric region. While the first species is more specialized on few plant items, the second showed a more varied and heterogeneous diet pattern among individuals. These differences might have been developed to avoid competition in the region of co-occurrence. Resource availability in the environment also seems to influence food choices. Our data indicate that C. minutus and C. flamarioni are generalist species, but that some preference for Poaceae, Asteraceae and Araliaceae families can be suggested for both rodents.

show abstract

“…By combining the identification of consumed items through DNA barcoding [23], [24] and next-generation sequencing (NGS), several authors have recently been able to determine the diet of animal species, both in carnivores (e.g. [22], [25]–[27]) and in herbivores [21], [24], [28]–[31]. To date, this approach has seldom been tested to characterize herbivory in tropical forest ecosystems [18], [32], [33].…”

Section: Introductionmentioning

confidence: 99%

“…Indeed, the P6 loop marker has universal primers in flowering plants, a short size of the target fragment (typically less than 100 bp) and high inter-specific variation in size and sequence [28]. If some a priori knowledge of the herbivore's diet is available, plant group-specific primers may also be used to refine the resolution of the analysis [20], [31], [33], [35]. Moreover, the recent development of high throughput sequencing technology [20] now allows the production of thousands of short-length sequences (e.g.…”

Section: Introductionmentioning

confidence: 99%

Unveiling the Diet of Elusive Rainforest Herbivores in Next Generation Sequencing Era? The Tapir as a Case Study

et al. 2013

Self Cite

View full text Add to dashboard Cite

Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.

show abstract

Assessment of the Food Habits of the Moroccan Dorcas Gazelle in M’Sabih Talaa, West Central Morocco, Using the trnL Approach

Cited by 64 publications

References 65 publications

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents

Unveiling the Diet of Elusive Rainforest Herbivores in Next Generation Sequencing Era? The Tapir as a Case Study

Contact Info

Product

Resources

About