Locating rearrangement events in a phylogeny based on highly fragmented assemblies

Abstract

BackgroundThe inference of genome rearrangement operations requires complete genome assemblies as input data, since a rearrangement can involve an arbitrarily large proportion of one or more chromosomes. Most genome sequence projects, especially those on non-model organisms for which no physical map exists, produce very fragmented assembles, so that a rearranged fragment may be impossible to identify because its two endpoints are on different scaffolds. However, breakpoints are easily identified, as long as they do not coincide with scaffold ends. For the phylogenetic context, in comparing a fragmented assembly with a number of complete assemblies, certain combinatorial constraints on breakpoints can be derived. We ask to what extent we can use breakpoint data between a fragmented genome and a number of complete genomes to recover all the arrangements in a phylogeny.ResultsWe simulate genomic evolution via chromosomal inversion, fragmenting one of the genomes into a large number of scaffolds to represent the incompleteness of assembly. We identify all the breakpoints between this genome and the remainder. We devise an algorithm which takes these breakpoints into account in trying to determine on which branch of the phylogeny a rearrangement event occurred. We present an analysis of the dependence of recovery rates on scaffold size and rearrangement rate, and show that the true tree, the one on which the rearrangement simulation was performed, tends to be most parsimonious in estimating the number of true events inferred.ConclusionsIt is somewhat surprising that the breakpoints identified just between the fragmented genome and each of the others suffice to recover most of the rearrangements produced by the simulations. This holds even in parts of the phylogeny disjoint from the lineage of the fragmented genome.

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2‐acidified sea water

“…Combined with a good BUSCO completeness measure, this indicates that our transcriptome is of high quality. While ~0.25% of the transcriptome significantly differentially expressed is a low percentage, it is similar to other studies using nontargeted investigations of the entire transcriptome: in a copepod in response to heat stress (0.88%; Schoville, Barreto, Moy, Wolff, & Burton, 2012), an Antarctic fish in response to pH and heat stress (0.08%–1.0%; Huth & Place, 2016), corals in response to heat stress (0.4%–0.7%; Barshis et al., 2013), and sea grass in response to heat stress (0.8%; Franssen et al., 2011). However, other studies have found greater percentages of the transcriptome affected (e.g., corals in response to low pH; 12%–19%; Moya, Huisman, & Ball, 2012; or heat shock; 27%; Seneca & Palumbi, 2015).…”

“…In a short‐term response to stress, an upregulation in CSR proteins (or a transcriptomic upregulation of genes coding for them) is expected (Tomanek & Somero, 2000; Kültz, 2003), as has been reported in numerous marine organisms (Lauritano, Procaccini, & Ianora, 2012; Tomanek, 2014; Huth & Place, 2016). However, several studies show both up‐ and downregulation of CSR‐related genes in response to a range of abiotic stressors (Anderson et al., 2015; Goncalves et al., 2016).…”

“…Huth and Place (2016) found that the degree of altered gene expression in fish exposed to pH and temperature stress decreased with time, being highest 7 days after the start of exposure and decreasing by 80%–90% at 28 and 56 days postexposure start (from 1.0% to 0.1% to 0.2%, respectively). Evans, Chan, Menge, and Hofmann (2013) found a strong reduction in the number of genes differentially expressed with time in purple sea urchin larvae ( Strongylocentrotus purpuratus ), from 153 at 44 hr of age to only five genes at 96 hr.…”

“…Raising wild oysters in low pH water for only three generations produced oysters that responded to low pH stress in the same way as the selectively bred line (selected for fast growth and disease immunity over seven generations), namely downregulation of stress genes (Parker et al., 2012). Similarly, gene expression of an Antarctic fish, whose adaptation to cold waters involves constitutively elevated stress‐related genes, shows a downregulation of those genes when exposed to temperature stress (Huth & Place, 2016). Heat‐tolerant strains of Daphnia pulex showed a general downregulation of genes involved in transcription, translation, DNA replication, DNA repair, and core metabolic pathways in response to heat stress, a response not present in heat‐sensitive strains (Yampolsky et al., 2014).…”

“…Calanus glacialis appears to increase the transcription of genes which upregulate the activity of these antiporters in response to low pH sea water. Other organisms upregulate sodium:proton antiporters in response to low pH water (fish: Catches, Burns, Edwards, & Claiborne, 2006; Huth & Place, 2016) or other ion pumps (sodium:potassium ATPase; Pan, Applebaum, & Manahan, 2015), while corals (Moya et al., 2012; Evans et al., 2013) and urchins (Todgham & Hofmann, 2009; Stumpp, Dupont, Thorndyke, & Melzner, 2011) did not upregulate them at low pH, potentially being able to regulate pH sufficiently with the existing antiporters. Our findings indicate that sodium:proton pumps were upregulated by C. glacialis nauplii in an attempt to maintain cellular pH homeostasis at low pH, although the wide range of altered gene expression at low pH indicates that they did not succeed in fully maintaining homeostasis.…”