Biology subjects

Hajibabaei, M.

Publications and source records attributed to Hajibabaei, M..

4 recordsLinked to original sources

bioRxiv2018

Over 2.5 million COI sequences in GenBank and growing

The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding warrants a careful look at the underlying reference databases used to make high-throughput taxonomic assignments. The objectives of this study are to document trends and assess the future usability of COI records for metabarcode identification. Over 2.5 million COI sequences were found in GenBank, half of which were fully identified to the species rank. From 2003 to 2017, the number of COI Eukaryote records deposited has grown by two orders of magnitude representing a nearly 42-fold increase in unique species. For fully identified records, 92% are at least 500 bp in length, 74% have a country annotation, and 51% have latitude-longitude annotations. To ensure the future usability of COI records in GenBank we suggest: 1) Improving the geographic representation of COI records 2) Improving the cross-referencing of COI records in the Barcode of Life Data System and GenBank to facilitate consolidation and incorporation into existing bioinformatic pipelines, 3) Adherence to the minimum information about a marker gene sequence guidelines, and 4) Integrating metabarcodes from eDNA and mixed community studies with existing sequences. COI metabarcoders are normally considered consumers of taxonomic data. Here we discuss the potential for taxonomists to reverse this pattern and instead mine metabarcode data to guide species discovery. The growth of COI reference records over the past 15 years has been substantial and is likely to be a resource across many fields for years to come.

ecology↗

bioRxiv2017

Automated high throughput animal DNA metabarcode classification

Until now, there has been difficulty assigning names to animal barcode sequences isolated directly from eDNA in a rapid, high-throughput manner, providing a measure of confidence for each assignment. To address this gap, we have compiled nearly 1 million marker gene DNA barcode sequences appropriate for classifying chordates, arthropods, and flag members of other major eukaryote groups. We show that the RDP naive Bayesian classifier can assign the same number of queries 19 times faster than the popular BLAST top hit method and reduce the false positive rate by two-thirds. As reference databases become more representative of current species diversity, confidence in taxonomic assignments should continue to improve. We recommend that investigators can improve the performance of species-level assignments immediately by supplementing existing reference databases with full-length DNA barcode sequences from representatives of local fauna.

bioinformatics↗

bioRxiv2017

DNA Metabarcoding For High-Throughput Monitoring Of Estuarine Macrobenthic Communities

Benthic communities are key components of aquatic ecosystems biomonitoring. However, morphology-based species identifications remain a low-throughput, and sometimes ambiguous, approach. Despite metabarcoding methodologies have been applied for above-species taxa inventories in marine meiofaunal communities, a comprehensive approach providing species-level identifications for estuarine macrobenthic communities is still lacking. Here we report a combination of experimental and field studies demonstrating the aptitude of COI metabarcoding to provide robust species-level identifications within a framework of high-throughput monitoring of estuarine macrobenthic communities. To investigate the ability to recover DNA barcodes from all species present in a bulk DNA extract, we assembled 3 phylogenetically diverse communities, using 4 different primer pairs to generate PCR products of the COI barcode region. Between 78 and 83% of the species in the tested communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct sites of an estuary. Our results indicate that the species richness would be considerably underestimated if only morphological methods were used. Although further refinement is required for improving the efficiency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifications in macrobenthos monitoring.

genetics↗

bioRxiv2016

Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples

Environmental DNA analysis using PCR amplified marker genes has been a key application of high-throughput sequencing (HTS). However, PCR bias is a major drawback to gain accurate qualitative and quantitative biodiversity data. We developed a PCR-free approach using enrichment baits for species-specific mitochondrial cytochrome c oxidase 1(COI) DNA barcodes. The sequence capture was tested on species-rich bulk terrestrial and aquatic benthic samples. Hybridization capture recovered an average of 6 and 4.7 more arthropod orders than amplicon sequencing for terrestrial and benthic samples, respectively. For the terrestrial sample, the four most abundant arthropod orders comprised 94.0% of the sample biomass. These same four orders comprised 95.5% and 97.5% of the COI sequences recovered by amplification and capture, respectively. Hybridization capture recovered three arthropod orders that were detected by biomass analysis, but not by amplicon sequencing and two other insect orders that were not detected by either biomass or amplicon methods. These results indicate the advantage of using sequence capture for a more accurate analysis of biodiversity in bulk environmental samples. The protocol can be easily customized to other DNA barcode markers or gene regions of interest for a wide range of taxa or for a specific target group.

genomics↗