A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

Putatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae)

Table S1. Sample information

Length, weight, smoltscale, sex and NKA activity for every fish sampled. Individuals included in the microarray analysis and incorporated into the microarray reference pool are identified. Numbers assigned to each sample during RNA purification, and names used for each sample in the Gene Expression Omnibus accession are also listed

photos

Archive of photographs of each individual fish in *.jpg format. Fish identification numbers correspond to Table S1

Table S2. Primer table.

qPCR targets, primers, amplicon sizes (bases) and efficiency percentages from Oncorhynchus mykiss standard curve

Additional File 1. Total differential gene lists.

Total differential gene lists for day 8 migrant compared to resident, pre-release smoltscale 3 compared to smoltscale 2, and resident day 48 compared to resident day 8

Table S3. Gene Ontology enrichment in migrants or residents.

Trimmed GO enrichment for the day eight migrant compared to resident gene lists (GO Trimming performed with an 0.80 soft trim threshold). BP = Biological Process; CC = Cellular Component; MF = Molecular Function

Data from: Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss

Divergent life history strategies occur in steelhead or rainbow trout Oncorhynchus mykiss, and many populations produce both migrant (anadromous fish that move to the ocean after rearing) and resident (do not migrate and remain in fresh water) individuals. Mechanisms leading to each type are only partially understood; while the general tendency of a population is heritable, individual tendency may be plastic, influenced by local environment. Steelhead hatchery programmes aim to mitigate losses in wild stocks by producing trout that will migrate to the ocean and not compete with wild trout for limited freshwater resources. To increase our understanding of gill function in these migratory or resident phenotypes, here we compare gill transcriptome profiles of hatchery-released fish either at the release site (residents) or five river kilometres downstream while still in full fresh water (migrants). To test whether any of these genes can be used as predictive markers for smoltification, we compared these genes between migrant-like and undifferentiated trout while still in the hatchery in a common environment (prerelease). Results confirmed the gradual process of smoltification, and the importance of energetics, gill remodelling and ion transport capacity for migrants. Additionally, residents overexpressed transcripts involved in antiviral defences, potentially for immune surveillance via dendritic cells in the gills. The best smoltification marker candidate was protein s100a4, expression of which was highly correlated with Na(+) , K(+) ATPase (NKA) activity and smolt-like morphology in pre- and postrelease trout gills

Additional File 1. Total differential gene lists.

Total differential gene lists for day 8 migrant compared to resident, pre-release smoltscale 3 compared to smoltscale 2, and resident day 48 compared to resident day 8

Table S3. Gene Ontology enrichment in migrants or residents.

Trimmed GO enrichment for the day eight migrant compared to resident gene lists (GO Trimming performed with an 0.80 soft trim threshold). BP = Biological Process; CC = Cellular Component; MF = Molecular Function

Table S1. Sample information

Length, weight, smoltscale, sex and NKA activity for every fish sampled. Individuals included in the microarray analysis and incorporated into the microarray reference pool are identified. Numbers assigned to each sample during RNA purification, and names used for each sample in the Gene Expression Omnibus accession are also listed