ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

Zhang, Zhang; Xiao, Jingfa; Wu, Jiayan; Zhang, Haiyan; Liu, Guiming; Wang, Xumin; Dai, Lin

doi:10.1016/j.bbrc.2012.02.101

Cited by 344 publications

(202 citation statements)

References 20 publications

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“…Otherwise the longest available partial sequence was selected. Filtered sequences were grouped by orthology using ParaAT1.0 102 , then aligned and translated using MACSE version 1.01b 103 with default parameters. In total, 11,254 groups of orthologous genes were retained for comparative genomic analyses (Supplementary Table 9).…”

Section: Comparative Genomic Analyses Orthologue Identification and mentioning

confidence: 99%

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

et al. 2017

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The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

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Section: Comparative Genomic Analyses Orthologue Identification and mentioning

confidence: 99%

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

et al. 2017

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“…Trees were drawn with iTOL (Letunic and Bork, 2011). A coding sequence alignment for Ka/Ks ratio estimation was prepared with ParaAT (Zhang et al, 2012b). The Ka/Ks ratio was calculated in KaKs_ Calculator using all of the implemented methods (Zhang et al, 2006), and this ratio was averaged over all the predictions.…”

Section: Tree Buildingmentioning

confidence: 99%

A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis

et al. 2015

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(A.J.).Linker (H1) histones play critical roles in chromatin compaction in higher eukaryotes. They are also the most variable of the histones, with numerous nonallelic variants cooccurring in the same cell. Plants contain a distinct subclass of minor H1 variants that are induced by drought and abscisic acid and have been implicated in mediating adaptive responses to stress. However, how these variants facilitate adaptation remains poorly understood. Here, we show that the single Arabidopsis (Arabidopsis thaliana) stressinducible variant H1.3 occurs in plants in two separate and most likely autonomous pools: a constitutive guard cell-specific pool and a facultative environmentally controlled pool localized in other tissues. Physiological and transcriptomic analyses of h1.3 null mutants demonstrate that H1.3 is required for both proper stomatal functioning under normal growth conditions and adaptive developmental responses to combined light and water deficiency. Using fluorescence recovery after photobleaching analysis, we show that H1.3 has superfast chromatin dynamics, and in contrast to the main Arabidopsis H1 variants H1.1 and H1.2, it has no stable bound fraction. The results of global occupancy studies demonstrate that, while H1.3 has the same overall binding properties as the main H1 variants, including predominant heterochromatin localization, it differs from them in its preferences for chromatin regions with epigenetic signatures of active and repressed transcription. We also show that H1.3 is required for a substantial part of DNA methylation associated with environmental stress, suggesting that the likely mechanism underlying H1.3 function may be the facilitation of chromatin accessibility by direct competition with the main H1 variants.Linker (H1) histones are conserved and ubiquitous structural components of eukaryotic chromatin required for the stabilization of higher order chromatin structure and are generally thought to restrict DNA accessibility. Interestingly, despite their architectural role, H1 histones were shown to be highly mobile and continuously exchanging among chromatin-binding sites (Raghuram et al., 2009). They are also the most variable of the histones, with numerous nonallelic variants coexisting in the same cell. In vertebrates, several evolutionarily conserved subfamilies of H1 can be distinguished (Talbert et al., 2012) and appear to play both redundant and specific roles during development and cellular differentiation (McBryant et al., 2010). There is accumulating evidence that, in animals, regulation of the proportions of H1 variants with different dynamic behavior in chromatin is involved in controlling the accessibility of DNA to trans-acting factors (Jullien et al., 2010;Shahhoseini et al., 2010;Zhang et al., 2012a;Pérez-Montero et al., 2013;Christophorou et al., 2014).Epigenetic mechanisms, including DNA and histone modifications and active nucleosome remodeling, are major players in translating signals about environmental perturbations into adaptive responses at the transc...

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“…In order to analyse the substitutions within the coding sequences of both pAsa2 and pAsa7, each nucleotide sequence was codon-aligned using MUSCLE version 3.8.31 (Edgar, 2004) through ParaAT.pl version 1.0 (Zhang et al, 2012). The synonymous and non-synonymous substitutions were evaluated by DAMBE version 6.1.6 (Xia, 2013).…”

Section: Methodsmentioning

confidence: 99%

Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida

et al. 2016

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Aeromonas salmonicida subsp. salmonicida is a fish pathogen known to have a rich plasmidome. In the present study, we discovered an isolate of this bacterium bearing an additional unidentified small plasmid. After having sequenced the DNA of that isolate by nextgeneration sequencing, it appeared that the new small plasmid is a ColE1-type replicon plasmid, named here pAsa7. This plasmid bears a functional chloramphenicol-acetyltransferase-encoding gene (cat-pAsa7) previously unknown in A. salmonicida and responsible for resistance to chloramphenicol. A comparison of pAsa7 with pAsa2, the only known ColE1-type replicon plasmid usually found in A. salmonicida subsp. salmonicida, revealed that even if both plasmids share a high structural similarity, it is still unclear if pAsa7 is a derivative of pAsa2 since they showed several mutations at the nucleotide level. Transcriptomic analysis revealed that the catpAsa4 gene, another chloramphenicol-acetyltransferase-encoding gene, found on the large plasmid pAsa4, was significantly more transcribed than cat-pAsa7. This was correlated with a higher chloramphenicol resistance for isolates bearing pAsa4 compared with the one having pAsa7. Finally, a phylogenetic analysis showed that both CAT-pAsa4 and CAT-pAsa7 proteins were in different clusters. The clustering was supported by the identity of residues involved in the catalytic site. In addition, to give a better understanding of the large drug-resistance panel of A.salmonicida, this study reinforces the hypothesis that A. salmonicida subsp. salmonicida is a considerable reservoir for mobile genetic elements such as plasmids.

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ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

Cited by 344 publications

References 20 publications

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis

Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida

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