Genome assembly at chromosome scale with telomere ends for Pearlspot, Etroplus suratensis

Abstract

The pearlspot, Etroplus suratensis is a climate resilient cichlid fish that exhibits unusual adaptation to salinity. The fish is able to complete full life cycle in diverse salinity habitats ranging from fresh water to marine environments. High-quality primary and phased genome assemblies were generated for pearlspot fish using PacBio HiFi and Arima HiC sequencing technologies, for the first time. The primary assembly is highly contiguous with contig N50 length of 36 Mb. The final assembly is of 1.247 Gb with N50 length of 51.57 Mb and 98% of the genome length anchored to 24 chromosomes. The genome was assessed to be 99.9% complete based on BUSCO evaluation and was predicted to contain 52.96% repeat elements. We have predicted 27,192 protein encoding genes, of which 21,580 were functionally annotated. The genome offers an invaluable resource to understand adaptation of pearlspot fish to diverse salinity habitats.

Fig. 1

A specimen of Etroplus suratensis.

Fig. 2

(a) Hi-C map representing the 24 Chromosomes of Etroplus suratensis genome assembly (b) Circos plot representation of the 24 chromosomes of Etroplus suratensis. From the outermost: Track1: The 24 chromosomes of the pearlspot genome. Track2: Contigs corresponding to the chromosomes represented as tiles. Track3: Representation of telomeric repeats in log scale at chromosome ends. Track4: Quality values (QV) across the chromosomes shown as line plot with red, yellow and green backgrounds representing ranges 0 - 20, 20 – 30 and 30 -100 respectively. Track5 - Track8: Major repeat elements, SINEs, LINEs, LTRs and DNA Transposons, respectively, shown as scatter plot with a 2 kb sliding window. Track9: Predicted protein-coding genes in chromosomes depicted as highlights with incremental gene lengths of 20 Kb [viz. <20 kb (Very dark orange), 20 kb - 40 kb (dark orange), 40 kb - 60 kb (orange), 60 kb - 80 kb (Light orange) and >80 kb (Green)]. Track10: GC content of pearlspot genome shown as line diagram plotted with 50 kb sliding window. The GC values below 35 and above 45 are shown in dark red color, and remaining in orange color.

Fig. 3

Genome size estimation profiles of Etroplus suratensis. (a) Flow cytometry principle. Histogram depicting the count of events for Etroplus suratensis blood cells and chicken erythrocytes. (b) Genome length assessment of Etroplus suratensis by k-mer frequency generated using Jellyfish and Genomescope.

Fig. 4

Etroplus suratensis mitochondrial genome map depicting the protein coding genes, D-loop, rRNA genes, tRNA genes, GC content and GC Skew.

Fig. 5

Completeness analysis using BUSCO for Etroplus suratensis genome against Actinopterygii_odb10 orthologous database.

Fig. 6

(a) Synteny map between Pearlspot and Spotted tilapia (b) Synteny map between Pearlspot and Nile tilapia.