![]() metabarcoding, by simultaneously DNA barcoding multiple species in complex samples. Recent advances in high-throughput sequencing (HTS) technologies brought this strategy to a new level, i.e. Among them, DNA barcoding enables identification of individual specimens through the amplification and sequencing of one (or several) taxonomically informative DNA sequence, called barcode sequence. The development of molecular techniques has opened new possibilities for plant identification. In addition, morphological identification relies on the analysis of tissues or even whole plants, which makes it inappropriate to study processed products. Despite being simple and cost-effective, these strategies rely on the experience of a few experts and the distinction between closely related specimens may not be possible. ![]() Traditionally, the identification of plant species has been carried out through morphological identification and via microscopic examination. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases. This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids ‘black box’ systems that are sometimes encountered. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. ![]() In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |