Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

The characteristics and phylogenetic relationship of two complete mitochondrial genomes of Cottus pollux (scorpaeniformes: cottidae)

We report two complete mitochondrial genomes of Cottus pollux based on specimens collected from Deokdong and Hoam Streams in the Republic of Korea. The two complete mitochondrial genomes were 16,558 and 16,557 bp long. Both contain the 37 standard genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region) in the same order and have similar nucleotide compositions. According to the phylogenetic tree constructed using the maximum-likelihood method, C. pollux is closely related to C. reinii. The genetic information provided by the complete mitochondrial genome of C. pollux will contribute to an understanding of the phylogenetic position, evolutionary relationships, and biogeographical patterns of this species within the genus Cottus.

Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.

A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data

Background

The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. 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. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. 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. 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.

Results

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. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. 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. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets.

Conclusion

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. 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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-022-01067-5.

Recombinant Mitochondrial Genomes Reveal Recent Interspecific Hybridization between Invasive Salangid Fishes

The interspecific recombination of the mitochondrial (mt) genome, if not an experimental artifact, may result from interbreeding of species with broken reproductive barriers, which, in turn, is a frequent consequence of human activities including species translocations, habitat modifications, and climate change. This issue, however, has not been addressed for Protosalanx chinensis and other commercially important and, simultaneously, invasive salangid fishes that were the product of successful aquaculture in China. To assess the probability of interspecific hybridization, we analyzed the patterns of diversity and recombination in the complete mitochondrial (mt) genomes of these fishes using the GenBank resources. A sliding window analysis revealed a non-uniform distribution of the intraspecific differences in P. chinensis with four highly pronounced peaks of divergence centered at the COI, ND4L-ND4, and ND5 genes, and also at the control region. The corresponding divergent regions in P. chinensis show a high sequence similarity (99−100%) to the related salangid fishes, Neosalanx tangkahkeii and N. anderssoni. This observation suggests that the divergent regions of P. chinensis may represent a recombinant mitochondrial DNA (mtDNA) containing mt genome fragments belonging to different salangid species. Indeed, four, highly significant (pairwise homoplasy index test, P < 0.00001) signals of recombination have been revealed at coordinates closely corresponding to the divergent regions. The recombinant fragments are, however, not fixed, and different mt genomes of P. chinensis are mosaic, containing different numbers of recombinant events. These facts, along with the high similarity or full identity of the recombinant fragments between the donor and the recipient sequences, indicate a recent interspecific hybridization between P. chinensis and two Neosalanx species. Alternative hypotheses, including taxonomical misidentifications, sequence misalignments, DNA contamination, and/or artificial PCR recombinants, are not supported by the data. The recombinant fragments revealed in our study represent diagnostic genetic markers for the identification and distinguishing of hybrids, which can be used to control the invasive dynamics of hybrid salangid fishes.

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.

Genetic Evidence for a Mixed Composition of the Genus Myoxocephalus (Cottoidei: Cottidae) Necessitates Generic Realignment

Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.

Complete mitochondrial genome of the surf smelt Hypomesus japonicus (Osmeriformes, Osmeridae)

The complete mitochondrial genome was sequenced in two individuals of the surf smelt Hypomesus japonicus. The genome sequences are 16,762 and 16,771 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mitochondrial genomes published previously. The difference between two H. japonicus genomes studied is 0.37%, which is noticeably higher in comparison with other osmerid fishes. The level of sequence divergence between H. japonicus and related osmerids belonging to genera Hypomeus, Osmerus, and Mallotus varies within a very narrow range (12.31-13.72%) indicating poor phylogenetic resolution of this complex fish group.

An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex

Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the "Mediterranean" (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the "African silver-leafing" (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the "ASL" does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies.