Gene_locus Report for: crigr-g3h7k6

(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.)
> cellular organisms: N E > Eukaryota: N E > Opisthokonta: N E > Metazoa: N E > Eumetazoa: N E > Bilateria: N E > Deuterostomia: N E > Chordata: N E > Craniata: N E > Vertebrata: N E > Gnathostomata: N E > Teleostomi: N E > Euteleostomi: N E > Sarcopterygii: N E > Dipnotetrapodomorpha: N E > Tetrapoda: N E > Amniota: N E > Mammalia: N E > Theria: N E > Eutheria: N E > Boreoeutheria: N E > Euarchontoglires: N E > Glires: N E > Rodentia: N E > Myomorpha: N E > Muroidea: N E > Cricetidae: N E > Cricetinae: N E > Cricetulus: N E > Cricetulus griseus: N E

Title: A reference genome of the Chinese hamster based on a hybrid assembly strategy
Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K and Lee KH <8 more author(s)> Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH (- 8)
Ref: Biotechnol Bioeng, 115:2087, 2018 : PubMed
Abstract


ESTHER: Rupp_2018_Biotechnol.Bioeng_115_2087
PubMedSearch: Rupp 2018 Biotechnol.Bioeng 115 2087
PubMedID: 29704459
Gene_locus related to this paper: crigr-g3h083, crigr-a0a3l7ib08, crigr-g3ifk5, crigr-g3h7k6

Abstract

Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read-based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.



        

Title: The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W and Palsson BO <12 more author(s)> Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO (- 12)
Ref: Nat Biotechnol, 29:735, 2011 : PubMed
Abstract


ESTHER: Xu_2011_Nat.Biotechnol_29_735
PubMedSearch: Xu 2011 Nat.Biotechnol 29 735
PubMedID: 21804562
Gene_locus related to this paper: crigr-g3hfm0, crigr-g3h894, crigr-a0a061hy43, crigr-g3h3f6, crigr-g3i9k7, crigr-g3i9k8, crigr-g3grm1, crigr-g3in33, crigr-g3i1j5, crigr-a0a061ika1, crigr-g3hqj0, crigr-g3hh02, crigr-g3h083, crigr-a0a3l7ib08, crigr-a0a061ihy9, crigr-g3ifk5, crigr-g3ily8, crigr-g3hvc7, crigr-g3gtp1, crigr-g3h7k6, crigr-g3hkm8

Abstract

Chinese hamster ovary (CHO)-derived cell lines are the preferred host cells for the production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45 Gb of genomic sequence, with 24,383 predicted genes. We associate most of the assembled scaffolds with 21 chromosomes isolated by microfluidics to identify chromosomal locations of genes. Furthermore, we investigate genes involved in glycosylation, which affect therapeutic protein quality, and viral susceptibility genes, which are relevant to cell engineering and regulatory concerns. Homologs of most human glycosylation-associated genes are present in the CHO-K1 genome, although 141 of these homologs are not expressed under exponential growth conditions. Many important viral entry genes are also present in the genome but not expressed, which may explain the unusual viral resistance property of CHO cell lines. We discuss how the availability of this genome sequence may facilitate genome-scale science for the optimization of biopharmaceutical protein production.