Genome sequencing and chromosome-level genome assembly
We obtained a total of 714,523,240 sequence reads from the Illumina PE
library, yielding a total sequence length of 100,539,703,234 bp
(Table S1 ). K-mer analysis (K = 17) indicated that the genome
size is 2.30 Gb with slightly repeats ratio (Figure S1 ). We
also generated 100.54 Gb raw data using the Nanopore platform (111.95×
coverage) for genome assembly: a data set of 13,970,063 reads with an
N50 of 22,905 bp (Table S2 ). To construct the chromosome-level
genome, 373.43 Gb Hi-C data were generated for scaffolding
(Table S3 ). The final assembled B. l. tsinlingensisgenome is summarized in Table S4-S5 . In this assembly, 414
scaffolds/chromosomes (>100 bp) were included, with a total
length of 2,031,709,341 bp. The N50 was 50.15 Mb, and the chromosome
mounting ratio was 99.58% (Figure 1A ). Although the published
genomes of salmonids are mostly at the chromosome level, our genome is
still comparable to other salmonids (Table S6 ). We also used
different strategies to evaluate the quality of this genome assembly,
including the assembled transcript mapping ratio from the RNA-seq data
of 5 different tissues/organs (Table S7-S9 ), BUSCO results
based on the Metazoan model sets and the Eukaryota model set
(Table S10 ), Illumina short reads mapping ratio (Table
S11 ), and the genomic synteny between B. l. tsinlingensis and 6
other salmonids (Figure S2-S7 ). All of these results indicated
that this genome has a high level of accuracy, continuity, and
connectivity.
Compared with other related species, the GC content of the genome and
CDS of B. l. tsinlingensis were assessed. The genome GC content
of all salmonids was similar and ranged from 43.03% to 43.55%, which
is slightly higher compared with outgroup species such as D.
rerio (36.60%), E. lucius (42.22%), and L. oculatus(39.59%) (Figure S8 ). The GC content of CDS of salmonids was
also similar and ranged from 54.19% to 55.21%, which is slightly
higher compared with outgroup species, such as D. rerio(49.85%), E. lucius (54.64%), and L. oculatus (53.25%)
(Figure S9 ). These findings may be explained by the WGD event
in the salmonids (salmonid-specific fourth vertebrate WGD, Ss4R) and
suggest that other characters in salmonids, such as gene structure, TEs,Hox gene clusters, and others, may also be similar among salmonid
fishes.