TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

“…Protein coding sequences (COI, H3) were aligned by translating to amino acid sequences and back translating to nucleotides in Translator X (Abascal et al. 2010). Protein coding sequences that contained stop codons were removed to eliminate potential nuclear mitochondrial genes (Song et al.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

et al. 2017

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Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are “evolutionary dead‐ends.” This implies that cave‐adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave‐dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave‐dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave‐dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a “dead‐end” for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.

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“…Multiple alignments of amino acid sequences were performed by clustalW2 with default options, and the resulting amino acid sequence alignments were used to guide the alignments of the nucleotide coding sequences using translatorX. 55 Then, the alignments were corrected manually and used for phylogenetic analyses. Phylogenetic trees of ATG4s and ATG8s were constructed using maximum likelihood method using MEGA 6.0.…”

Section: Phylogenetic Analysis and Data Visualizationmentioning

confidence: 99%

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

et al. 2016

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Autophagy is important for degradation and recycling of intracellular components. In a diversity of genera and species, orthologs and paralogs of the yeast Atg4 and Atg8 proteins are crucial in the biogenesis of double-membrane autophagosomes that carry the cellular cargoes to vacuoles and lysosomes. Although many plant genome sequences are available, the ATG4 and ATG8 sequence analysis is limited to some model plants. We identified 28 ATG4 and 116 ATG8 genes from the available 18 different plant genome sequences. Gene structures and protein domain sequences of ATG4 and ATG8 are conserved in plant lineages. Phylogenetic analyses classified ATG8s into 3 subgroups suggesting divergence from the common ancestor. The ATG8 expansion in plants might be attributed to whole genome duplication, segmental and dispersed duplication, and purifying selection. Our results revealed that the yeast Atg4 processes Arabidopsis ATG8 but not human LC3A (HsLC3A). In contrast, HsATG4B can process yeast and plant ATG8s in vitro but yeast and plant ATG4s cannot process HsLC3A. Interestingly, in Nicotiana benthamiana plants the yeast Atg8 is processed compared to HsLC3A. However, HsLC3A is processed when coexpressed with HsATG4B in plants. Molecular modeling indicates that lack of processing of HsLC3A by plant and yeast ATG4 is not due to lack of interaction with HsLC3A. Our in-depth analyses of ATG4 and ATG8 in the plant lineage combined with results of cross-kingdom ATG8 processing by ATG4 further support the evolutionarily conserved maturation of ATG8. Broad ATG8 processing by HsATG4B and lack of processing of HsLC3A by yeast and plant ATG4s suggest that the cross-kingdom ATG8 processing is determined by ATG8 sequence rather than ATG4.

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TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Cited by 1,239 publications

References 20 publications

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

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