Oncorhynchus mykiss gairdneri strain:Keithly Creek | breed:Interior Columbia Basin; Snake River drainage | cultivar:Redband Trout Genome sequencing and assembly

Currently, we are working towards generating a rainbow trout pan-genome reference that will better represent the genetic diversity in this species using de-novo chromosome level assemblies. To that end we have previously generated the reference genome from the Arlee line (USDA_OmykA_1.1; GCA_013265735.3), an improved assembly for the Swanson line (Omyk_2.0; GCA_025558465.1), and a genome assembly from the Whale Rock Male line (USDA_OmyWR_1.0; GCA_029834435.1). The Swanson YY male line was originated from a semi-domesticated resident fish from the Kenai Peninsula in Alaska with a haploid number of 29 chromosomes. The Arlee doubled haploid YY male line has a different genetic background from the Swanson line. It was originated from a well-known domesticated hatchery strain that was originally collected from the northern California coast. It has a haploid number of 32 chromosomes. The three Swanson chromosomes that are being divided to two acrocentric chromosomes are Omy04, 14 and 25. The Whale Rock line is also a YY male. Like the Arlee line, it has 2N=64 chromosomes and it was originated from the Central California Coast. The one known major difference is that it was originated from a wild fish from a landlocked steelhead population. The current de-novo chromosome level assembly is from a Keithley Creek (KC) male rainbow trout. The KC is from the inland lineage of rainbow trout (O. m. gairdneri) in contrast to the three previous assemblies that were done using fish from the coastal lineage (O. m. irideus). It is also known as Redband trout, with geographic distribution from the Interior Columbia Basin; Snake River Drainage. The KC is a resident population of Redband trout from the Montane ecosystem in contrast with the desert Redband trout. The exact Karyotype of the KC population is unknown. Our de-novo chromosome level genome assembly for the KC line provides strong support for 2N=60 number of chromosomes. The sex determination gene (sdY) is located on Chromosome 29. With the aim of establishing a homozygous line, the Keithley Creek line was prepared using the established protocol to induce androgenesis at Washington State University through irradiation of eggs obtained from an aquaculture stock and fertilization of the irradiated eggs with milt from a single wild Keithley Creek rainbow trout male which was followed by hydrostatic pressure shock to block the first cell cleavage of the fertilized eggs. However, since our DNA sequences mapping analysis in the process of the genome assembly indicated higher level of heterozygosity than in the established doubled haploid rainbow trout lines, we are obligated to caution that in the process that was used to establish the Keithley Creek line at Washington State University there might have been an inadvertent maternal contribution from the donor of the irradiated eggs, which was an aquaculture strain of rainbow trout possibly from a coastal origin. Hence this genome may not be considered a pure representative of the gairdneri inland lineage of rainbow trout.

本研究正基于从头染色体水平组装（de-novo chromosome level assemblies）构建虹鳟泛基因组参考序列，以更精准地刻画该物种的遗传多样性。为此，我们此前已完成Arlee品系（USDA_OmykA_1.1；GCA_013265735.3）的参考基因组构建、Swanson品系的优化基因组组装（Omyk_2.0；GCA_025558465.1），以及Whale Rock雄性品系的基因组组装（USDA_OmyWR_1.0；GCA_029834435.1）。
Swanson YY雄性品系源自阿拉斯加基奈半岛的半驯化定居型虹鳟，单倍体染色体数为29。
Arlee双单倍体（doubled haploid）YY雄性品系的遗传背景与Swanson品系存在显著差异：其源自知名的驯化孵化场品系，最初采集自加利福尼亚州北部海岸，单倍体染色体数为32。
Swanson品系的3条染色体将被拆分为2条近端着丝粒染色体（acrocentric chromosomes），分别为Omy04、Omy14与Omy25。
Whale Rock品系同样为YY雄性，与Arlee品系一致，染色体数为2N=64，源自加利福尼亚州中部海岸；已知的核心差异在于，该品系源自内陆硬头鳟（steelhead）种群的野生个体。
本次从头染色体水平组装的样本取自Keithley Creek（KC）雄性虹鳟：KC属于虹鳟内陆谱系（*Oncorhynchus mykiss gairdneri*），而此前的3组组装均采用了海岸谱系（*Oncorhynchus mykiss irideus*）的个体。该内陆谱系也被称为红带鳟（Redband trout），地理分布范围涵盖哥伦比亚内陆盆地与斯内克河流域。
KC种群为山地生态系统中的红带鳟定居种群，与沙漠红带鳟有所区别；目前尚未明确KC种群的确切核型（Karyotype）。
我们针对KC品系的从头染色体水平基因组组装结果，强有力地支持其染色体数为2N=60。
性别决定基因（sdY）位于29号染色体上。
为构建纯合品系，华盛顿州立大学采用已成熟的雄核发育（androgenesis）诱导方案培育Keithley Creek品系：先对水产养殖种群来源的卵进行辐照，再用单只野生KC雄性虹鳟的精液对辐照后的卵进行受精，随后通过静水压休克（hydrostatic pressure shock）阻断受精卵的第一次卵裂（cell cleavage）。
但在基因组组装过程中，我们通过DNA序列比对（DNA sequences mapping）分析发现，该品系的杂合度（heterozygosity）水平高于已报道的双单倍体虹鳟品系。因此我们特此提醒：华盛顿州立大学在培育KC品系的过程中，辐照卵的供体为水产养殖品系虹鳟（可能源自海岸谱系），可能存在意外的母本贡献。
因此，本基因组不能被视为虹鳟*Oncorhynchus mykiss gairdneri*内陆谱系的纯代表性样本。