Comparative genomics

  • Article
    | Open Access

    Teff is an indigenous cereal critical to food security in the Horn of Africa. Here, the authors report an improved genome assembly and observe the surprisingly low levels of large-scale structural rearrangement, homoeologous exchanges, or bias gene loss after the formation of this tetraploid species.

    • Robert VanBuren
    • , Ching Man Wai
    • , Xuewen Wang
    • , Jeremy Pardo
    • , Alan E. Yocca
    • , Hao Wang
    • , Srinivasa R. Chaluvadi
    • , Guomin Han
    • , Douglas Bryant
    • , Patrick P. Edger
    • , Joachim Messing
    • , Mark E. Sorrells
    • , Todd C. Mockler
    • , Jeffrey L. Bennetzen
    •  & Todd P. Michael
  • Article
    | Open Access

    Dingoes evolved in isolation from both their domesticated and wild ancestors. Here, the authors investigate the genomic basis of the feralization of dingoes and trace their origin to domestic dogs that migrated to Australia approximately 8300 years ago.

    • Shao-jie Zhang
    • , Guo-Dong Wang
    • , Pengcheng Ma
    • , Liang-liang Zhang
    • , Ting-Ting Yin
    • , Yan-hu Liu
    • , Newton O. Otecko
    • , Meng Wang
    • , Ya-ping Ma
    • , Lu Wang
    • , Bingyu Mao
    • , Peter Savolainen
    •  & Ya-ping Zhang
  • Article
    | Open Access

    Mikania micrantha is an extremely fast-growing invasive plant species that can cause serious damage to natural ecosystems. Here, the authors assemble its chromosome-scale reference genome and explore possible mechanisms that contribute to its rapid growth.

    • Bo Liu
    • , Jian Yan
    • , Weihua Li
    • , Lijuan Yin
    • , Ping Li
    • , Hanxia Yu
    • , Longsheng Xing
    • , Minling Cai
    • , Hengchao Wang
    • , Mengxin Zhao
    • , Jin Zheng
    • , Feng Sun
    • , Zhenzhen Wang
    • , Zhaoyang Jiang
    • , Qiaojing Ou
    • , Shubin Li
    • , Lu Qu
    • , Qilei Zhang
    • , Yaping Zheng
    • , Xi Qiao
    • , Yu Xi
    • , Yan Zhang
    • , Fan Jiang
    • , Cong Huang
    • , Conghui Liu
    • , Yuwei Ren
    • , Sen Wang
    • , Hangwei Liu
    • , Jianyang Guo
    • , Haihong Wang
    • , Hui Dong
    • , Changlian Peng
    • , Wanqiang Qian
    • , Wei Fan
    •  & Fanghao Wan
  • Article
    | Open Access

    Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.

    • Dasen Xie
    • , Yuanchao Xu
    • , Jinpeng Wang
    • , Wenrui Liu
    • , Qian Zhou
    • , Shaobo Luo
    • , Wu Huang
    • , Xiaoming He
    • , Qing Li
    • , Qingwu Peng
    • , Xueyong Yang
    • , Jiaqing Yuan
    • , Jigao Yu
    • , Xiyin Wang
    • , William J. Lucas
    • , Sanwen Huang
    • , Biao Jiang
    •  & Zhonghua Zhang
  • Article
    | Open Access

    Widely distributed red algae have experienced massive genome reduction during evolution. Here, using an improved genome assembly of Porphyridium purpureum, Lee et al. show the role of endosymbiotic gene transfer in plastid evolution and the correlation between phycobilisome linker diversification and the red algal radiation.

    • JunMo Lee
    • , Dongseok Kim
    • , Debashish Bhattacharya
    •  & Hwan Su Yoon
  • Article
    | Open Access

    Comparative genomic analysis of human and primate relatives can reveal important biological and evolutionary insights. Here, the authors present a long-read assembly of the Chinese rhesus macaque genome and identify ape-specific structural variants.

    • Yaoxi He
    • , Xin Luo
    • , Bin Zhou
    • , Ting Hu
    • , Xiaoyu Meng
    • , Peter A. Audano
    • , Zev N. Kronenberg
    • , Evan E. Eichler
    • , Jie Jin
    • , Yongbo Guo
    • , Yanan Yang
    • , Xuebin Qi
    •  & Bing Su
  • Article
    | Open Access

    Hyphae are a major innovation in fungi associated with transitions to multicellularity. Here, Kiss and colleagues use comparative genomic analyses to reconstruct the evolutionary origins of hyphae and the molecular evolution of hypha morphogenesis genes.

    • Enikő Kiss
    • , Botond Hegedüs
    • , Máté Virágh
    • , Torda Varga
    • , Zsolt Merényi
    • , Tamás Kószó
    • , Balázs Bálint
    • , Arun N. Prasanna
    • , Krisztina Krizsán
    • , Sándor Kocsubé
    • , Meritxell Riquelme
    • , Norio Takeshita
    •  & László G. Nagy
  • Article
    | Open Access

    The Chloropicophyceae represent an important group of green algae in tropical oceans, but there is only limited genomic resource available. Here, the authors present the genome sequence of Chloropicon primus, revealing a diploid structure and the presence of a propionate detoxification pathway.

    • Claude Lemieux
    • , Monique Turmel
    • , Christian Otis
    •  & Jean-François Pombert
  • Article
    | Open Access

    Recurrent urinary tract infections occur in ~ 25% of women. Here, Beatson and colleagues use whole genome sequencing to track the dynamics of an E. coli ST131 clone in a single patient over a 5-year period. This study provides unique insights into pathogen evolution during recurrent urinary infection.

    • Brian M. Forde
    • , Leah W. Roberts
    • , Minh-Duy Phan
    • , Kate M. Peters
    • , Brittany A. Fleming
    • , Colin W. Russell
    • , Sara M. Lenherr
    • , Jeremy B. Myers
    • , Adam P. Barker
    • , Mark A. Fisher
    • , Teik-Min Chong
    • , Wai-Fong Yin
    • , Kok-Gan Chan
    • , Mark A. Schembri
    • , Matthew A. Mulvey
    •  & Scott A. Beatson
  • Article
    | Open Access

    While multiple cotton genomes are available, genome wide variation comparison between allotetraploid upland cotton cultivars remain unexplored. Here, the authors assemble two upland cotton cultivars and reveal large scale structural variations on chromosome A08.

    • Zhaoen Yang
    • , Xiaoyang Ge
    • , Zuoren Yang
    • , Wenqiang Qin
    • , Gaofei Sun
    • , Zhi Wang
    • , Zhi Li
    • , Ji Liu
    • , Jie Wu
    • , Ye Wang
    • , Lili Lu
    • , Peng Wang
    • , Huijuan Mo
    • , Xueyan Zhang
    •  & Fuguang Li
  • Article
    | Open Access

    Chromatin is folded into Topologically Associating domains (TADs), with the organization and folding hierarchy of the TADs being highly dynamic. Here the authors develop a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency encounters present in Hi-C data within and between TADs and reconstruct TADs across cell differentiation, revealing local chromatin re-organization.

    • O. Shukron
    • , V. Piras
    • , D. Noordermeer
    •  & D. Holcman
  • Article
    | Open Access

    Existing apple genome assemblies all derive from Golden Delicious. Here, the authors combine different sequencing technologies to assemble a high quality genome of an anther-derived homozygous genotype HFTH1 and find the association of a retrotransposon and red fruit colour.

    • Liyi Zhang
    • , Jiang Hu
    • , Xiaolei Han
    • , Jingjing Li
    • , Yuan Gao
    • , Christopher M. Richards
    • , Caixia Zhang
    • , Yi Tian
    • , Guiming Liu
    • , Hera Gul
    • , Dajiang Wang
    • , Yu Tian
    • , Chuanxin Yang
    • , Minghui Meng
    • , Gaopeng Yuan
    • , Guodong Kang
    • , Yonglong Wu
    • , Kun Wang
    • , Hengtao Zhang
    • , Depeng Wang
    •  & Peihua Cong
  • Article
    | Open Access

    Broomcorn millet is one of the earliest domesticated plants and has the highest water use efficiency among cereals. Here, the authors report its genome assembly and annotation, which provides a valuable resource for breeders and paves the way for studying plant drought tolerance and C4 photosynthesis.

    • Changsong Zou
    • , Leiting Li
    • , Daisuke Miki
    • , Delin Li
    • , Qiming Tang
    • , Lihong Xiao
    • , Santosh Rajput
    • , Ping Deng
    • , Li Peng
    • , Wei Jia
    • , Ru Huang
    • , Meiling Zhang
    • , Yidan Sun
    • , Jiamin Hu
    • , Xing Fu
    • , Patrick S. Schnable
    • , Yuxiao Chang
    • , Feng Li
    • , Hui Zhang
    • , Baili Feng
    • , Xinguang Zhu
    • , Renyi Liu
    • , James C. Schnable
    • , Jian-Kang Zhu
    •  & Heng Zhang
  • Article
    | Open Access

    Broomcorn millet is one of the oldest crops cultivated by human that has strong abiotic stress tolerance. To facilitate genome assisted breeding of this and related species, the authors report its genome assembly and conduct comparative genome structure and evolution analyses with foxtail millet.

    • Junpeng Shi
    • , Xuxu Ma
    • , Jihong Zhang
    • , Yingsi Zhou
    • , Minxuan Liu
    • , Liangliang Huang
    • , Silong Sun
    • , Xiangbo Zhang
    • , Xiang Gao
    • , Wei Zhan
    • , Pinghua Li
    • , Lun Wang
    • , Ping Lu
    • , Haiming Zhao
    • , Weibin Song
    •  & Jinsheng Lai
  • Article
    | Open Access

    Despite technological advances, chromosome-level assemblies of mammalian genomes are still rare. Here, the authors use PacBio, Chicago and Hi-C approaches to generate a highly contiguous and partially-phased genome assembly for the water buffalo, Bubalus bubalis

    • Wai Yee Low
    • , Rick Tearle
    • , Derek M. Bickhart
    • , Benjamin D. Rosen
    • , Sarah B. Kingan
    • , Thomas Swale
    • , Françoise Thibaud-Nissen
    • , Terence D. Murphy
    • , Rachel Young
    • , Lucas Lefevre
    • , David A. Hume
    • , Andrew Collins
    • , Paolo Ajmone-Marsan
    • , Timothy P. L. Smith
    •  & John L. Williams
  • Article
    | Open Access

    Due to various structural and sequence complexities, the human Y chromosome is challenging to sequence and characterize. Here, the authors develop a strategy to sequence native, unamplified flow sorted Y chromosomes with a nanopore sequencing platform, and report the first assembly of a human Y chromosome of African origin.

    • Lukas F. K. Kuderna
    • , Esther Lizano
    • , Eva Julià
    • , Jessica Gomez-Garrido
    • , Aitor Serres-Armero
    • , Martin Kuhlwilm
    • , Regina Antoni Alandes
    • , Marina Alvarez-Estape
    • , David Juan
    • , Heath Simon
    • , Tyler Alioto
    • , Marta Gut
    • , Ivo Gut
    • , Mikkel Heide Schierup
    • , Oscar Fornas
    •  & Tomas Marques-Bonet
  • Article
    | Open Access

    Candida auris is an emergent fungal pathogen that is resistant to multiple antifungals. Here, Muñoz et al. analyse genomic sequences for isolates from each of the four major C. auris clades and for three related species, and identify genetic features associated with virulence, antifungal resistance and mating.

    • José F. Muñoz
    • , Lalitha Gade
    • , Nancy A. Chow
    • , Vladimir N. Loparev
    • , Phalasy Juieng
    • , Elizabeth L. Berkow
    • , Rhys A. Farrer
    • , Anastasia P. Litvintseva
    •  & Christina A. Cuomo
  • Article
    | Open Access

    During early embryogenesis, critical cardiac specification events occur. Here the authors isolate cardiac progenitor cells from early zebrafish embryos and characterize accessible chromatin regions specific to this cell population, finding that many of these regions overlap with conserved non-coding elements that are ortholgous to accessible chromatin regions in human.

    • Xuefei Yuan
    • , Mengyi Song
    • , Patrick Devine
    • , Benoit G. Bruneau
    • , Ian C. Scott
    •  & Michael D. Wilson
  • Article
    | Open Access

    Cis-regulatory elements are important factors for morphological changes. Here, the authors show widespread divergence of limb and eye regulatory elements in limb loss in snakes and eye degeneration in subterranean mammals respectively.

    • Juliana G. Roscito
    • , Katrin Sameith
    • , Genis Parra
    • , Bjoern E. Langer
    • , Andreas Petzold
    • , Claudia Moebius
    • , Marc Bickle
    • , Miguel Trefaut Rodrigues
    •  & Michael Hiller
  • Article
    | Open Access

    Sweetpotato is an important food security crop providing rich source of macro- and micronutrients including carbohydrates and vitamins. Here, the authors assemble of the two diploid relatives of cultivated sweetpotato and identify genes and alleles associated with carotenoid biosynthesis from breeding lines.

    • Shan Wu
    • , Kin H. Lau
    • , Qinghe Cao
    • , John P. Hamilton
    • , Honghe Sun
    • , Chenxi Zhou
    • , Lauren Eserman
    • , Dorcus C. Gemenet
    • , Bode A. Olukolu
    • , Haiyan Wang
    • , Emily Crisovan
    • , Grant T. Godden
    • , Chen Jiao
    • , Xin Wang
    • , Mercy Kitavi
    • , Norma Manrique-Carpintero
    • , Brieanne Vaillancourt
    • , Krystle Wiegert-Rininger
    • , Xinsun Yang
    • , Kan Bao
    • , Jennifer Schaff
    • , Jan Kreuze
    • , Wolfgang Gruneberg
    • , Awais Khan
    • , Marc Ghislain
    • , Daifu Ma
    • , Jiming Jiang
    • , Robert O. M. Mwanga
    • , Jim Leebens-Mack
    • , Lachlan J. M. Coin
    • , G. Craig Yencho
    • , C. Robin Buell
    •  & Zhangjun Fei
  • Article
    | Open Access

    The evolutionary forces that favour transitions in sex chromosomes are not well understood. Here, Jeffries and colleagues show a very high rate of sex chromosome turnover in true frogs, which may be driven by rapid mutation-load accumulation due to the low recombination rate in males.

    • Daniel L. Jeffries
    • , Guillaume Lavanchy
    • , Roberto Sermier
    • , Michael J. Sredl
    • , Ikuo Miura
    • , Amaël Borzée
    • , Lisa N. Barrow
    • , Daniele Canestrelli
    • , Pierre-André Crochet
    • , Christophe Dufresnes
    • , Jinzhong Fu
    • , Wen-Juan Ma
    • , Constantino Macías Garcia
    • , Karim Ghali
    • , Alfredo G. Nicieza
    • , Ryan P. O’Donnell
    • , Nicolas Rodrigues
    • , Antonio Romano
    • , Íñigo Martínez-Solano
    • , Ilona Stepanyan
    • , Silvia Zumbach
    • , Alan Brelsford
    •  & Nicolas Perrin
  • Article
    | Open Access

    The origin and evolution of separate sexes in plants are long-standing questions. Here, the authors use genus-wide sequencing to identify sex determining candidate genes in the genus Phoenix and demonstrate the consistence with the previously proposed two-mutation model.

    • Maria F. Torres
    • , Lisa S. Mathew
    • , Ikhlak Ahmed
    • , Iman K. Al-Azwani
    • , Robert Krueger
    • , Diego Rivera-Nuñez
    • , Yasmin A. Mohamoud
    • , Andrew G. Clark
    • , Karsten Suhre
    •  & Joel A. Malek
  • Article
    | Open Access

    The rapidly evolving Y chromosome accumulates male-benefit genes but is often poorly characterized in many mammals. Here, the authors assemble the male specific region of the horse Y chromosome and investigate its evolution and function.

    • Jan E. Janečka
    • , Brian W. Davis
    • , Sharmila Ghosh
    • , Nandina Paria
    • , Pranab J. Das
    • , Ludovic Orlando
    • , Mikkel Schubert
    • , Martin K. Nielsen
    • , Tom A. E. Stout
    • , Wesley Brashear
    • , Gang Li
    • , Charles D. Johnson
    • , Richard P. Metz
    • , Al Muatasim Al Zadjali
    • , Charles C. Love
    • , Dickson D. Varner
    • , Daniel W. Bellott
    • , William J. Murphy
    • , Bhanu P. Chowdhary
    •  & Terje Raudsepp
  • Article
    | Open Access

    Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.

    • Giulia I. M. Pasquesi
    • , Richard H. Adams
    • , Daren C. Card
    • , Drew R. Schield
    • , Andrew B. Corbin
    • , Blair W. Perry
    • , Jacobo Reyes-Velasco
    • , Robert P. Ruggiero
    • , Michael W. Vandewege
    • , Jonathan A. Shortt
    •  & Todd A. Castoe
  • Article
    | Open Access

    Dodders (Cuscuta spp., Convolvulaceae) are root- and leafless parasitic plants. Here, the authors sequence the genome of Cuscuta australis and find remarkable gene loss associated with parasitic lifestyle and large changes in body plan.

    • Guiling Sun
    • , Yuxing Xu
    • , Hui Liu
    • , Ting Sun
    • , Jingxiong Zhang
    • , Christian Hettenhausen
    • , Guojing Shen
    • , Jinfeng Qi
    • , Yan Qin
    • , Jing Li
    • , Lei Wang
    • , Wei Chang
    • , Zhenhua Guo
    • , Ian T. Baldwin
    •  & Jianqiang Wu
  • Article
    | Open Access

    It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.

    • Camille Clerissi
    • , Marie Touchon
    • , Delphine Capela
    • , Mingxing Tang
    • , Stéphane Cruveiller
    • , Clémence Genthon
    • , Céline Lopez-Roques
    • , Matthew A. Parker
    • , Lionel Moulin
    • , Catherine Masson-Boivin
    •  & Eduardo P. C. Rocha
  • Article
    | Open Access

    Giant viruses are visible by light microscopy and have unusually long genomes. Here, the authors report three new members of the Pandoraviridae family and investigate their evolution and diversity.

    • Matthieu Legendre
    • , Elisabeth Fabre
    • , Olivier Poirot
    • , Sandra Jeudy
    • , Audrey Lartigue
    • , Jean-Marie Alempic
    • , Laure Beucher
    • , Nadège Philippe
    • , Lionel Bertaux
    • , Eugène Christo-Foroux
    • , Karine Labadie
    • , Yohann Couté
    • , Chantal Abergel
    •  & Jean-Michel Claverie
  • Article
    | Open Access

    Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.

    • Rebecca E. O’Connor
    • , Michael N. Romanov
    • , Lucas G. Kiazim
    • , Paul M. Barrett
    • , Marta Farré
    • , Joana Damas
    • , Malcolm Ferguson-Smith
    • , Nicole Valenzuela
    • , Denis M. Larkin
    •  & Darren K. Griffin
  • Article
    | Open Access

    Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.

    • Jordi Paps
    •  & Peter W. H. Holland
  • Article
    | Open Access

    Selaginella lepidophylla is a clubmoss with extreme desiccation tolerance. Here, the authors assemble its highly heterozygotic haplotypes and examine gene expression changes during desiccation, which shed light on the mechanisms for maintaining a small genome size and adaptation to extreme drying.

    • Robert VanBuren
    • , Ching Man Wai
    • , Shujun Ou
    • , Jeremy Pardo
    • , Doug Bryant
    • , Ning Jiang
    • , Todd C. Mockler
    • , Patrick Edger
    •  & Todd P. Michael
  • Article
    | Open Access

    Horticultural lettuce varieties vary considerably in phenotype. Here, via RNA-seq of 240 different lettuce accessions, the authors identify loci and expression patterns associated with flavonoid and anthocyanin content and show that cultivated lettuce likely arose via a single domestication event.

    • Lei Zhang
    • , Wenqing Su
    • , Rong Tao
    • , Weiyi Zhang
    • , Jiongjiong Chen
    • , Peiyao Wu
    • , Chenghuan Yan
    • , Yue Jia
    • , Robert M. Larkin
    • , Dean Lavelle
    • , Maria-Jose Truco
    • , Sebastian Reyes Chin-Wo
    • , Richard W. Michelmore
    •  & Hanhui Kuang
  • Article
    | Open Access

    The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.

    • Sean P. Gordon
    • , Bruno Contreras-Moreira
    • , Daniel P. Woods
    • , David L. Des Marais
    • , Diane Burgess
    • , Shengqiang Shu
    • , Christoph Stritt
    • , Anne C. Roulin
    • , Wendy Schackwitz
    • , Ludmila Tyler
    • , Joel Martin
    • , Anna Lipzen
    • , Niklas Dochy
    • , Jeremy Phillips
    • , Kerrie Barry
    • , Koen Geuten
    • , Hikmet Budak
    • , Thomas E. Juenger
    • , Richard Amasino
    • , Ana L. Caicedo
    • , David Goodstein
    • , Patrick Davidson
    • , Luis A. J. Mur
    • , Melania Figueroa
    • , Michael Freeling
    • , Pilar Catalan
    •  & John P. Vogel
  • Article
    | Open Access

    The canonical scenario of sex chromosome evolution is through the differentiation of ancestral pairs of autosomes. Here, Fraïsse and colleagues use a comparative genomic analysis that shows the deep conservation of the Z chromosome in Lepidoptera and supports a non-canonical origin of the W chromosome.

    • Christelle Fraïsse
    • , Marion A. L. Picard
    •  & Beatriz Vicoso
  • Article
    | Open Access

    Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

    • Pedro H. Oliveira
    • , Marie Touchon
    • , Jean Cury
    •  & Eduardo P. C. Rocha
  • Article
    | Open Access

    High-quality reference genomes facilitate analysis of genome structure and variation. Here Duet al. create a near-complete assembly of the indicarice genome by combining single molecule sequencing with mapping data and fosmid sequences and identify genetic variants by comparison with other rice genomes.

    • Huilong Du
    • , Ying Yu
    • , Yanfei Ma
    • , Qiang Gao
    • , Yinghao Cao
    • , Zhuo Chen
    • , Bin Ma
    • , Ming Qi
    • , Yan Li
    • , Xianfeng Zhao
    • , Jing Wang
    • , Kunfan Liu
    • , Peng Qin
    • , Xin Yang
    • , Lihuang Zhu
    • , Shigui Li
    •  & Chengzhi Liang
  • Article
    | Open Access

    Batrachochytrium dendrobatidis and B. salamandrivoransare both important pathogens of amphibians, but they differ in their host ranges, infection strategies, and host immune responses. Here, Farrer and colleagues compare their genomes and transcriptomes to identify the genetic basis of these differences.

    • Rhys A. Farrer
    • , An Martel
    • , Elin Verbrugghe
    • , Amr Abouelleil
    • , Richard Ducatelle
    • , Joyce E. Longcore
    • , Timothy Y. James
    • , Frank Pasmans
    • , Matthew C. Fisher
    •  & Christina A. Cuomo
  • Article
    | Open Access

    The fungal Ascomycota provide a model phylum to investigate the evolution of complex multicellularity. Here, the authors combine genome sequencing with comparative and functional genomics to identify diverse endomembrane related machineries associated with the gain and loss of fungal complexity.

    • Tu Anh Nguyen
    • , Ousmane H. Cissé
    • , Jie Yun Wong
    • , Peng Zheng
    • , David Hewitt
    • , Minou Nowrousian
    • , Jason E. Stajich
    •  & Gregory Jedd
  • Article
    | Open Access

    Shotgun DNA sequencing experiments for microbial genomic analysis are often impractical due to minimum sample input requirements. Here the authors develop a microfluidic sample preparation platform that reduces sample input requirements 100-fold and enables high throughput sequencing from low numbers of cells.

    • Soohong Kim
    • , Joachim De Jonghe
    • , Anthony B. Kulesa
    • , David Feldman
    • , Tommi Vatanen
    • , Roby P. Bhattacharyya
    • , Brittany Berdy
    • , James Gomez
    • , Jill Nolan
    • , Slava Epstein
    •  & Paul C. Blainey
  • Article
    | Open Access

    Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleraceareference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits

    • Agnieszka A. Golicz
    • , Philipp E. Bayer
    • , Guy C. Barker
    • , Patrick P. Edger
    • , HyeRan Kim
    • , Paula A. Martinez
    • , Chon Kit Kenneth Chan
    • , Anita Severn-Ellis
    • , W. Richard McCombie
    • , Isobel A. P. Parkin
    • , Andrew H. Paterson
    • , J. Chris Pires
    • , Andrew G. Sharpe
    • , Haibao Tang
    • , Graham R. Teakle
    • , Christopher D. Town
    • , Jacqueline Batley
    •  & David Edwards
  • Article
    | Open Access

    Snakes have many characteristics that distinguish them from their relatives. Here, Yin et al. sequence the genome of the five-pacer viper, Deinagkistrodon acutus, and use comparative genomic analyses to elucidate the evolution of transposable elements, developmental genes and sex chromosomes in snakes.

    • Wei Yin
    • , Zong-ji Wang
    • , Qi-ye Li
    • , Jin-ming Lian
    • , Yang Zhou
    • , Bing-zheng Lu
    • , Li-jun Jin
    • , Peng-xin Qiu
    • , Pei Zhang
    • , Wen-bo Zhu
    • , Bo Wen
    • , Yi-jun Huang
    • , Zhi-long Lin
    • , Bi-tao Qiu
    • , Xing-wen Su
    • , Huan-ming Yang
    • , Guo-jie Zhang
    • , Guang-mei Yan
    •  & Qi Zhou
  • Article
    | Open Access

    The ascomycete Cenococcum geophilum is a beneficial mycorrhizal symbiont found frequently on tree roots. Here the authors use comparative genomics and transcriptomics to define genomic signatures that differentiate the beneficial C. geophilumfrom its saprotrophic and pathogenic relatives.

    • Martina Peter
    • , Annegret Kohler
    • , Robin A. Ohm
    • , Alan Kuo
    • , Jennifer Krützmann
    • , Emmanuelle Morin
    • , Matthias Arend
    • , Kerrie W. Barry
    • , Manfred Binder
    • , Cindy Choi
    • , Alicia Clum
    • , Alex Copeland
    • , Nadine Grisel
    • , Sajeet Haridas
    • , Tabea Kipfer
    • , Kurt LaButti
    • , Erika Lindquist
    • , Anna Lipzen
    • , Renaud Maire
    • , Barbara Meier
    • , Sirma Mihaltcheva
    • , Virginie Molinier
    • , Claude Murat
    • , Stefanie Pöggeler
    • , C. Alisha Quandt
    • , Christoph Sperisen
    • , Andrew Tritt
    • , Emilie Tisserant
    • , Pedro W. Crous
    • , Bernard Henrissat
    • , Uwe Nehls
    • , Simon Egli
    • , Joseph W. Spatafora
    • , Igor V. Grigoriev
    •  & Francis M. Martin
  • Article
    | Open Access

    Mutualisms in which ants protect plants in exchange for food and shelter have arisen independently multiple times. Here, Rubin and Moreau sequence the genomes of three mutualistic ant species and four of their non-mutualistic relatives and show that the transition to mutualism is associated with elevated evolutionary rates across the genome

    • Benjamin E. R. Rubin
    •  & Corrie S. Moreau
  • Article
    | Open Access

    Nitrogen fixation in oceans is facilitated by associations between marine phytoplankton and cyanobacteria such as UCYN-A. Here, Cornejo-Castillo et al. show that UCYN-A diversified in the late Cretaceous under strong purifying selection to become lineage-specific symbiont partners with different prymnesiophytes.

    • Francisco M. Cornejo-Castillo
    • , Ana M. Cabello
    • , Guillem Salazar
    • , Patricia Sánchez-Baracaldo
    • , Gipsi Lima-Mendez
    • , Pascal Hingamp
    • , Adriana Alberti
    • , Shinichi Sunagawa
    • , Peer Bork
    • , Colomban de Vargas
    • , Jeroen Raes
    • , Chris Bowler
    • , Patrick Wincker
    • , Jonathan P. Zehr
    • , Josep M. Gasol
    • , Ramon Massana
    •  & Silvia G. Acinas
  • Article
    | Open Access

    Toxoplasma gondii is a parasite that causes zoonotic infections in humans. Here, the authors identify tandem amplification and diversification of secretory pathogenesis determinants in the T. gondiigenome and show that clade-specific inheritance of conserved haploblocks enriched for these determinants shapes population structure.

    • Hernan Lorenzi
    • , Asis Khan
    • , Michael S. Behnke
    • , Sivaranjani Namasivayam
    • , Lakshmipuram S. Swapna
    • , Michalis Hadjithomas
    • , Svetlana Karamycheva
    • , Deborah Pinney
    • , Brian P. Brunk
    • , James W. Ajioka
    • , Daniel Ajzenberg
    • , John C. Boothroyd
    • , Jon P. Boyle
    • , Marie L. Dardé
    • , Maria A. Diaz-Miranda
    • , Jitender P. Dubey
    • , Heather M. Fritz
    • , Solange M. Gennari
    • , Brian D. Gregory
    • , Kami Kim
    • , Jeroen P. J. Saeij
    • , Chunlei Su
    • , Michael W. White
    • , Xing-Quan Zhu
    • , Daniel K. Howe
    • , Benjamin M. Rosenthal
    • , Michael E. Grigg
    • , John Parkinson
    • , Liang Liu
    • , Jessica C. Kissinger
    • , David S. Roos
    •  & L. David Sibley
  • Article |

    Insect gustatory and olfactory receptor genes encode transmembrane proteins that detect diverse chemicals, but their evolutionary origins are unclear. This study identifies homologues of these genes in non-Bilateria and reveals an unexpected role for one in sea anemone embryonic development.

    • Michael Saina
    • , Henriette Busengdal
    • , Chiara Sinigaglia
    • , Libero Petrone
    • , Paola Oliveri
    • , Fabian Rentzsch
    •  & Richard Benton
  • Article |

    Comparative genomics can provide valuable insights on adaptations to hostile environments. Here, the authors sequence the genomes and transcriptomes of the Bactrian camel, dromedary and alpaca, to reveal the demographic history of the group as well as metabolic adaptations to the desert environment.

    • Huiguang Wu
    • , Xuanmin Guang
    • , Mohamed B. Al-Fageeh
    • , Junwei Cao
    • , Shengkai Pan
    • , Huanmin Zhou
    • , Li Zhang
    • , Mohammed H. Abutarboush
    • , Yanping Xing
    • , Zhiyuan Xie
    • , Ali S. Alshanqeeti
    • , Yanru Zhang
    • , Qiulin Yao
    • , Badr M. Al-Shomrani
    • , Dong Zhang
    • , Jiang Li
    • , Manee M. Manee
    • , Zili Yang
    • , Linfeng Yang
    • , Yiyi Liu
    • , Jilin Zhang
    • , Musaad A. Altammami
    • , Shenyuan Wang
    • , Lili Yu
    • , Wenbin Zhang
    • , Sanyang Liu
    • , La Ba
    • , Chunxia Liu
    • , Xukui Yang
    • , Fanhua Meng
    • , Shaowei Wang
    • , Lu Li
    • , Erli Li
    • , Xueqiong Li
    • , Kaifeng Wu
    • , Shu Zhang
    • , Junyi Wang
    • , Ye Yin
    • , Huanming Yang
    • , Abdulaziz M. Al-Swailem
    •  & Jun Wang
  • Article
    | Open Access

    The African chironomid midge, Polypedilum vanderplanki, is able to withstand extreme desiccation. Here the authors sequence the genomes of a desiccation-tolerant and desiccation-sensitive species of chironomid midge and pinpoint genes that may have a role in conferring resistance to desiccation.

    • Oleg Gusev
    • , Yoshitaka Suetsugu
    • , Richard Cornette
    • , Takeshi Kawashima
    • , Maria D. Logacheva
    • , Alexey S. Kondrashov
    • , Aleksey A. Penin
    • , Rie Hatanaka
    • , Shingo Kikuta
    • , Sachiko Shimura
    • , Hiroyuki Kanamori
    • , Yuichi Katayose
    • , Takashi Matsumoto
    • , Elena Shagimardanova
    • , Dmitry Alexeev
    • , Vadim Govorun
    • , Jennifer Wisecaver
    • , Alexander Mikheyev
    • , Ryo Koyanagi
    • , Manabu Fujie
    • , Tomoaki Nishiyama
    • , Shuji Shigenobu
    • , Tomoko F. Shibata
    • , Veronika Golygina
    • , Mitsuyasu Hasebe
    • , Takashi Okuda
    • , Nori Satoh
    •  & Takahiro Kikawada
  • Article
    | Open Access

    Rice false smut, caused by the pathogenic ascomycete fungus Ustilaginoidea virens (Cooke) Takah, has a significant economic impact on crop production. Here, Zhang et al. report the draft genome sequence of U. virensand provide insight into the evolution of genes involved in pathogenicity and adaptation to a biotrophic and floret-infecting lifestyle.

    • Yong Zhang
    • , Kang Zhang
    • , Anfei Fang
    • , Yanqing Han
    • , Jun Yang
    • , Minfeng Xue
    • , Jiandong Bao
    • , Dongwei Hu
    • , Bo Zhou
    • , Xianyun Sun
    • , Shaojie Li
    • , Ming Wen
    • , Nan Yao
    • , Li-Jun Ma
    • , Yongfeng Liu
    • , Min Zhang
    • , Fu Huang
    • , Chaoxi Luo
    • , Ligang Zhou
    • , Jianqiang Li
    • , Zhiyi Chen
    • , Jiankun Miao
    • , Shu Wang
    • , Jinsheng Lai
    • , Jin-Rong Xu
    • , Tom Hsiang
    • , You-Liang Peng
    •  & Wenxian Sun
  • Article
    | Open Access

    Common tobacco (Nicotiana tabacum) is a widely cultivated and economically important non-food crop. Here, the authors report the draft genome sequences for three of the most common tobacco varieties and provide insights into the evolution of tobacco through a comparative analysis with closely related species.

    • Nicolas Sierro
    • , James N.D. Battey
    • , Sonia Ouadi
    • , Nicolas Bakaher
    • , Lucien Bovet
    • , Adrian Willig
    • , Simon Goepfert
    • , Manuel C. Peitsch
    •  & Nikolai V. Ivanov
  • Article
    | Open Access

    Despite major conservation efforts, the Yangtze river dolphin, or baiji, is now recognised as functionally extinct. Here, Zhou et al. report a high quality draft baiji genome, as well as three re-sequenced genomes, and highlight evolutionary adaptations to aquatic life.

    • Xuming Zhou
    • , Fengming Sun
    • , Shixia Xu
    • , Guangyi Fan
    • , Kangli Zhu
    • , Xin Liu
    • , Yuan Chen
    • , Chengcheng Shi
    • , Yunxia Yang
    • , Zhiyong Huang
    • , Jing Chen
    • , Haolong Hou
    • , Xuejiang Guo
    • , Wenbin Chen
    • , Yuefeng Chen
    • , Xiaohong Wang
    • , Tian Lv
    • , Dan Yang
    • , Jiajian Zhou
    • , Bangqing Huang
    • , Zhengfei Wang
    • , Wei Zhao
    • , Ran Tian
    • , Zhiqiang Xiong
    • , Junxiao Xu
    • , Xinming Liang
    • , Bingyao Chen
    • , Weiqing Liu
    • , Junyi Wang
    • , Shengkai Pan
    • , Xiaodong Fang
    • , Ming Li
    • , Fuwen Wei
    • , Xun Xu
    • , Kaiya Zhou
    • , Jun Wang
    •  & Guang Yang