2020

Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication
Nong, Wenyan & Qu, Zhe & Li, Yiqian & Owen, Tom & Wong, Annette & Yip, Ho & Lee, Hoi & Narayana, Satya & Baril, Tobias & Swale, Thomas & Jianquan, Cao & Chan, Ting-Fung & Kwan, Hoi & Ngai, Sai & Panagiotou, Gianni & Qian, Pei-Yuan & Qiu, Jian-Wen & Yip, Kevin & Ismail, Noraznawati & Hui, Jerome.
https://doi.org/10.1101/2020.04.16.045815

Deeply conserved synteny resolves early events in vertebrate evolution
Simakov, O., Marlétaz, F., Yue, J. et al.
Nat Ecol Evol 4, 820-830 (2020). https://doi.org/10.1038/s41559-020-1156-z

De novo assembly of the cattle reference genome with single-molecule sequencing
Rosen B, Bickhart D, Schnabel R, et al.
GigaScience, Volume 9, Issue 3, March 2020, giaa021, https://doi.org/10.1093/gigascience/giaa021

The giant sequoia genome and proliferation of disease resistance gene
Scott, Alison & Zimin, Aleksey & Puiu, Daniela & Workman, Rachael & Britton, Monica & Zaman, Sumaira & Caballero, Madison & Read, Andrew & Bogdanove, Adam & Burns, Emily & Wegrzyn, Jill & Timp, Winston & Salzberg, Steven & Neale, David.
https://doi.org/10.1101/2020.03.17.995944

Chromosomal-level reference genome of the incense tree Aquilaria sinensis
Nong W, Law STS, Wong AYP, Baril T, Swale T, Chu LM, Hayward A, Lau DTW, Hui JHL.
Mol Ecol Resour. 2020 Mar 10. https://doi.org/10.1111/1755-0998.13154

High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia.
Louha S, Ray DA, Winker K, Glenn TC
G3 (Bethesda). 2020 Feb 19. pii: g3.400929.2019. https://doi.org/10.1534/g3.119.400929

A draft genome sequence of the elusive giant squid, Architeuthis dux.
Gilbert T et al.,
GigaScience, Volume 9, Issue 1, January 2020. https://doi.org/10.1093/gigascience/giz152

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins
Somasekar Seshagiri et al.,
Nature Genetics Jan 2020. https://doi.org/10.1038/s41588-019-0559-8

A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise
Miriam Schreiber, Martin Mascher, Jonathan Wright, Sudharasan Padmarasu, Axel Himmelbach, Darren Heavens, Linda Milne, Bernardo J. Clavijo, Nils Stein and Robbie Waugh
G3: GENES, GENOMES, GENETICS Early online April 2, 2020; ; https://doi.org/10.1534/g3.119.401010

2019

Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequencing and Hi-C analysis
Park et al.,
Molecular Ecology Resources 2019. https://doi.org/10.1111/1755-0998.13132

Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel
Grabek, K.R., Cooke, T.F., Epperson, L.E. et al.,
Commun Bio 2, 478 (2019). https://doi.org/10.1038/s42003-019-0719-5

Genome sequence and analysis of the eggplant (Solanum melongena L.)
Dandan Li, et al.,
doi: https://doi.org/10.1101/824540

A highly contiguous reference genome for northern bobwhite (Colinus virginianus)
Salter et al.
G3 (Bethesda) 2019 Oct 14; Pre-print. https://doi.org/10.1534/g3.119.400609

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data
Ellie E. Armstrong, Ryan W. Taylor, Danny E. Miller, Christopher Kaelin, Gregory Barsh, Elizabeth A. Hadly, Dmitri Petrov
July 2019. doi: https://doi.org/10.1101/705483

A reference-grade wild soybean genome
Xie, M., Chung, C.Y., Li, M. et al.
Nat Commun. 10, 1216 (2019) doi: https://doi.org/10.1038/s41467-019-09142-9

Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids
Raudsepp T  et al.
Front. Genet., 21 June 2019 https://doi.org/10.3389/fgene.2019.00586

De Novo Genome Sequence Assembly of Dwarf Coconut (Cocos nucifera L. ‘Catigan Green Dwarf’) Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species
Galvez HF  et al.
G3: GENES, GENOMES, GENETICS August 1, 2019 vol. 9 no. 8 2377-2393; https://doi.org/10.1534/g3.119.400215

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary
Elbers JP, Rogers MF, Perelman PL, et al.
Mol Ecol Resour 2019;19:1015–1026; https://doi.org/10.1111/1755-0998.13020

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Edger PP et al.
Gigascience 8, 2019, 1–15; https://doi.org/10.1093/gigascience/giz012

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
Williams JL et al.
Nat Commun. 2019 Jan 16; https://doi.org/10.1038/s41467-018-08260-0

2018

Improved reference genome for the domestic horse increases assembly contiguity and composition
MacLeod JN et al.
Commun Biol. 2018 Nov 16; https://doi.org/10.1038/s42003-018-0199-z

Comparative analysis of the Pocillopora damiconis genome highlights roles of immune system in coral evolution
Cunning, R., Bay, R.A., Gillette, P. et al.
Scientific Reports. 8, 16134 (2018); https://doi.org/10.1038/s41598-018-34459-8

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
Lilue J, Doran AG, Fiddes IT, et al.
Nat Genet. 2018;50(11):1574-1583; https://doi.org/10.1038/s41588-018-0223-8

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves
Powell D, Subramanian S, Suwansa-Ard S, et al.
DNA Res. 2018;25(6):655-665; https://doi.org/10.1093/dnares/dsy032

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves
Powell D, Subramanian S, Suwansa-Ard S, et al.
DNA Res. 2018;25(6):655-665; https://doi.org/10.1093/dnares/dsy032

Chicago and Dovetail Hi-C proximity ligation yield chromosome length scaffolds of Ixodes scapularis genome
Nuss A, Sharma A, Gulia-Nuss M.
bioRxiv 392126; https://doi.org/10.1101/392126

Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution
Shu-Miaw Chaw, Yu-Ching Liu, Han-Yu Wang, Yu-Wei Wu, Chan-Yi Ivy Lin, Chung-Shien Wu, Huei-Mien Ke, Lo-Yu Chang, Chih-Yao Hsu, Hui-Ting Yang, Edi Sudianto, Ming-Hung Hsu, Kun-Pin Wu, Ning-Ni Wang, Jim Leebens-Mack, Isheng. J. Tsai
bioRxiv 371112; https://doi.org/10.1101/371112

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars.
Thind AK, Wicker T, Müller T, et al.
Genome Biol 2018;19(1):104. Published 2018 Aug 17; https://doi.org/10.1186/s13059-018-1477-2

Decimation by sea star wasting disease and rapid genetic change in a keystone species, Pisaster ochraceus.
Schiebelhut LM, Puritz JB, Dawson MN.
Proc Natl Acad Sci U S A. 2018;115(27):7069-7074; https://doi.org/10.1073/pnas.1800285115

The African Bullfrog (Pyxicephalus adspersus) genome unites the two ancestral ingredients for making vertebrate sex chromosomes.
Denton RD, Kudra RS, Malcom JW, Du Preez L, Malone JH.
bioRxiv 329847; https://doi.org/10.1101/329847

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

A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library.
Hoffberg SL, Troendle NJ, Glenn TC, et al.
G3 (Bethesda). 2018;8(6):1855-1861. Published 2018 May 31; https://doi.org/10.1534/g3.118.200101

High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena ).
Autenrieth, Mm, Hartmann, S, Lah, L, Roos, A, Dennis, AB, Tiedemann, R.
Mol Ecol Resour. 2018; 18: 1469– 1481; https://doi.org/10.1111/1755-0998.12932

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.
Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M, et al.
Nat Ecol Evol. 2018; 2(4):659-668; https://doi.org/10.1038/s41559-018-0476-8

EquCab3, an Updated Reference Genome for the Domestic Horse
Kalbfleisch TS, Rice ES, DePriest Jr. MS, Walenz BP, Hestand MS, Vermeesch JR, O’Connell BL, Fiddes IT, Vershinina AO, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN
Nat Genet. 2018;50(2):270-277; https://doi.org/10.1101/306928

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution [published correction appears in Nat Genet. 2018 Apr 19;:] [published correction appears in Nat Genet. 2018 Nov;50(11):1617].
Smith JJ, Timoshevskaya N, Ye C, et al.
bioRxiv 306928; https://doi.org/10.1038/s41588-017-0036-1

Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii).
Fernandez-Silva I, Henderson JB, Rocha LA, Simison WB.
Sci Rep. 2018;8(1):1498. Published 2018 Jan 24; https://doi.org/10.1038/s41598-018-19430-x

2017

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0).
Kuderna LFK, Tomlinson C, Hillier LW, et al.
Gigascience. 2017;6(11):1-6; https://doi.org/0.1093/gigascience/gix098

A critical comparison of technologies for a plant genome sequencing project.
Paajanen P, Kettleborough G, López-Girona E, Giolai M, Heavens D, Baker D, Lister A, Wilde G, Hein I, Macaulay I, Bryan GJ, Clark MD
bioRxiv 201830; https://doi.org/10.1101/201830

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