Dovetail Genomicsの最近の論文集

先日Dovetail GenomicsのHi-Cの話をしたので、今日は、論文リストを紹介
投稿中のものも含まれます。色んな生物ゲノムが読まれているんだなあ・・・

Dovetail Genomics Current Publications !!

【Genome Assembly】

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)
Holt C et al. G3 (Bethesda). 2018 May 4;8(5):1391-1398. doi: 10.1534/g3.117.300443.

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
Smith JJ et al. Nat Genet. 2018 May;50(5):768. doi: 10.1038/s41588-018-0075-2.

A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library
Hoffberg SL et al. G3 (Bethesda). 2018 Apr 27. pii: g3.200101.2018. doi:10.1534/g3.118.200101.

EquCab3, an Updated Reference Genome for the Domestic Horse
Kalbfleisch TS et al. 2018 Apr 25; Pre-print*.

High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)
Autenrieth M et al. 2018 Apr 19; Pre-print*.

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat
Medoza MLZ et al. Nat Ecol Evol. 2018 Apr;2(4):659-668. doi: 10.1038/s41559-018-0476-8.

Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
Fernandez-Silva I et al. Sci Rep. 2018 Jan 24;8(1):1498. doi: 10.1038/s41598-018-19430-x.

Genetic architecture drives seasonal onset of hibernation in the 13-lined ground squirrel
Grabek KR et al. 2017 Dec 2; Pre-print*.

The draft genome of tropical fruit durian (Durio zibethinus)
Teh BT et al. Nat Genet. 2017 Nov;49(11):1633-1641. doi: 10.1038/ng.3972.

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
Moll KM et al. BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4.

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly
Thind AK et al. Nat Biotechnol. 2017 Aug;35(8):793-796. doi: 10.1038/nbt.3877.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Schwager EE et al. BMC Biol. 2017 Jul 31;15(1):62. doi: 10.1186/s12915-017-0399-x.

The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants
Nallu S et al. 2017 Jun 23; Pre-print*.

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
Rice ES et al. Genome Res. 2017 May;27(5):686-696. doi: 10.1101/gr.213595.116.

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
Jiao WB et al. Genome Res. 2017 May;27(5):778-786. doi: 10.1101/gr.213652.116.

The impact of third generation genomic technologies on plant genome assembly
Jaio WB & Scheeberger K. Curr Opin Plant Biol. 2017 Apr;36:64-70. doi:10.1016/j.pbi.2017.02.002.

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Reyes-Chin-Wo S et al. Nat Commun. 2017 Apr 12;8:14953. doi: 10.1038/ncomms14953.

The genome of Chenopodium quinoa
Jarvis DE et al. Nature. 2017 Feb 16;542(7641):307-312. doi: 10.1038/nature21370.

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
Pootakham W et al. Sci Rep. 2017 Feb 2;7:41457. doi: 10.1038/srep41457.

Genome evolution in the allotetraploid frog Xenopus laevis
Session AM et al. Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity
Bredeson JV et al. Nat Biotechnol. 2016 May;34(5):562-70. doi: 10.1038/nbt.3535.

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Putnam N et al. Genome Res. 2016 Mar;26(3):342-50. doi: 10.1101/gr.193474.115.

【FixC & Selva】
Structural variation detection by proximity ligation from FFPE tumor tissue
Troll C et al. 2018 Feb 27; Pre-print*.

*Pre-print articles available on bioRxiv

あと、ついでといっては失礼ですが、来週12日（火）にイルミナ社のウェブセミナーで、理研の工樂さんによるHi-Cのお話があります。
私は立場上、イルミナ社の宣伝したら怒られますが（笑）、これは純粋にゲノムサイエンス&技術の話なので良いかと。
興味のあるかたはどうぞ！