RT Journal Article
T1 A long reads-based
 de-novo
 assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout
A1 Gao. Guangtu
A1 Magadán Mompó, Susana
A1 Waldbieser, Geoffrey C
A1 Youngblood, Ramey C
A1 Wheeler, Paul A
A1 Scheffler, Brian E
A1 Thorgaard, Gary H
A1 Palti, Yniv
K1 2401.14-4 Taxonomía Animal. Peces
K1 2409 Genética
K1 2412 Inmunología
AB Currently, 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 (2 N = 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 shown through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.
PB G3 Genes|Genome|Genetics
SN 21601836
YR 2021
FD 2021-02-22
LK http://hdl.handle.net/11093/2463
UL http://hdl.handle.net/11093/2463
LA eng
NO G3 Genes|Genome|Genetics, 11(4): 1-11 (2021)
NO USDA Agricultural Research Service | Ref. 8082-31000-012
DS Investigo
RD 05-oct-2024