Differentiation within the Drawida ghilarovi complex (Moniligastridae: Annelida) revealed by multigene transcriptomic dataset analysis

Shekhovtsov, Sergei V.; Shipova, Aleksandra A.; Булахова, Н. А.; Берман, Д. И.

doi:10.1016/j.ejsobi.2022.103411

Cited by 3 publications

(1 citation statement)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to the application of transcriptomes to evolutionary developmental biology, the transcriptomes of various annelid lineages are obtained to infer deep phylogenetic relationships ( Weigert et al, 2014 ; Andrade et al, 2015 ; Struck et al, 2015 ; Helm et al, 2018 ; Erséus et al, 2020 ; Martín-Durán et al, 2021 ; Tilic et al, 2022 ) since the phylogenetic relationships of higher taxa in annelids were not sufficiently resolved in phylogenies based on several genes. Transcriptomes are also used for the phylogenetic analyses of interfamilial relationships of closely related families and intrafamilial relationships of annelids ( Lemer et al, 2015 ; Novo et al, 2016 ; Anderson et al, 2017 ; Stiller et al, 2020 ; Tilic et al, 2020b ; Shekhovtsov et al, 2022 ). Also, there has been an increase in the number of studies that employ genome skimming for phylogenetic analyses based on mitogenomes in recent years ( Richter et al, 2015 ; Bernardino et al, 2017 ; Zhang et al, 2018 ; Zhao et al, 2022 ; Struck et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Kobayashi

2023

PeerJ

View full text Add to dashboard Cite

Background The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA. Methods The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank. Results and Discussion mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22–24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.

show abstract

Section: Introductionmentioning

confidence: 99%

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Kobayashi

2023

PeerJ

View full text Add to dashboard Cite

show abstract

Biochemical response of two earthworm taxa exposed to freezing

et al. 2023

View full text Add to dashboard Cite

Catalogue of the moniligastrid earthworms (Clitellata, Moniligastrida, Moniligastridae) of the world

NARAYANAN,

PALIWAL,

THOMAS

et al. 2024

Zootaxa

View full text Add to dashboard Cite

This study presents a comprehensive catalogue of the moniligastrid earthworms (Moniligastrida, Moniligastridae) of the world. A total of 176 valid species/subspecies belonging to 5 genera are known to exist in this primitive family. Drawida is the speciose genus with 147 species/subspecies. Of the various moniligastrids, three species of Drawida are considered as peregrine outside its normal Asian range. Among the valid species, occurrence of 30.68% are known only from the type locality. It is noteworthy that the types of 125 (71.02%) species are currently known to exist in various repositories around the world. The existence of the remaining species can only be inferred from the literature since their types are either non-existent, missing, dried out, or lost. Present catalogue includes valid scientific names, synonyms, type locality, type respository details along with registration number, geographic distribution pattern within its native range, and references.

show abstract

Differentiation within the Drawida ghilarovi complex (Moniligastridae: Annelida) revealed by multigene transcriptomic dataset analysis

Cited by 3 publications

References 28 publications

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Biochemical response of two earthworm taxa exposed to freezing

Catalogue of the moniligastrid earthworms (Clitellata, Moniligastrida, Moniligastridae) of the world

Contact Info

Product

Resources

About