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Supplemental Material for Gao et al., 2021
online resource
posted on 2021-02-16, 17:53 authored by Guangtu Gao, Susana Magadan, Geoffrey C. Waldbieser, Ramey C. Youngblood, Paul A. Wheeler, Brian E. Scheffler, Gary H. Thorgaard, Yniv PaltiCurrently, there is still a need to improve the contiguity of the
rainbow trout reference genome and to use multiple genetic backgrounds that
will represent the genetic diversity of this species. The Arlee doubled haploid
line was originated from a domesticated hatchery strain that was originally
collected from the northern California coast. The Canu pipeline was used to
generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads
sequence data. The assembly was further improved with Bionano optical maps and
Hi-C proximity ligation sequence data to generate 32 major scaffolds
corresponding to the karyotype of the Arlee line (2N=64). It is composed of 938
scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ~95% was
in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In
rainbow trout the haploid chromosome number can vary from 29 to 32. In the
Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04,
14 and 25 are divided into six acrocentric chromosomes. Additional structural
variations that were identified in the Arlee genome included the major
inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions
that will require further validation. This is also the first rainbow trout
genome assembly that includes a scaffold with the sex-determination gene (sdY)
in the chromosome Y sequence. The
utility of this genome assembly is demonstrated through the improved annotation
of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12
and Omy13.