Lineage‐Specific and Highly Derived Gene Sequences Among Amoebozoa, Revealed by the Comparative Analysis of Transcriptomes from Twelve Amoebozoan Species

• Published in: The Journal of eukaryotic microbiology Vol. 64; no. 5; pp. 622 - 631
• Main Authors: Bondarenko, Natalya I., Bondarenko, Anton S., Smirnov, Alexey V.
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.09.2017
• Subjects: Amoebozoa - classification; Amoebozoa - genetics; Comparative analysis; Deoxyribonucleic acid; DNA; DNA barcoding; DNA Barcoding, Taxonomic - methods; DNA sequencing; Environmental DNA; Evolution, Molecular; Gene Expression Profiling - methods; Gene families; Genes; lineage‐specific genes; metagenomics; molecular ecology; Molecular Sequence Annotation; Phylogeny; Proteins; Protists; Protozoan Proteins - genetics; Sequence Analysis, DNA - methods; Sequencing; Species; Species Specificity; Surveys; Taxonomy; lineage-specific genes; molecular ecology; metagenomics; DNA barcoding
• ISSN: 1066-5234; 1550-7408
• DOI: 10.1111/jeu.12397

Amoebozoa represent a difficult group for traditional morphology‐based taxonomy. Molecular approaches, such as gene sequencing and DNA barcoding have greatly enhanced our knowledge of the diversity of these organisms. However, metagenomic studies of Amoebozoa still did not provide as impressive results as they did among some other groups of protists. In environmental DNA surveys done on fragments of SSU rDNA gene and other traditional DNA barcodes, Amoebozoa genes normally constitute a minor part of the total gene diversity and represent only the most abundant lineages. A potential way to resolve this problem is the usage of DNA barcodes based on genes, which are unique or highly derived in this group of organisms. In the present study, we attempted to find such genes and gene families with a low level of paralogy, potentially appropriate as Amoebozoa‐specific DNA barcodes. For this we re‐assembled transcriptomes of 12 amoebozoan species available from the public databases and performed gene annotation and identification of orthologous genes. In our analysis Amoebozoa‐specific and highly derived sequences formed 53,182 clusters of orthologs, containing from 2 to 299 proteins each. Some of these genes may be a potential target for DNA barcoding of Amoebozoa.