Genome Evolution And Environmental Adaption Of Echinochloa Species In Poaceae

The genus Echinochloa belongs to family Poaceae.As a common weed in paddy fields,barnyard grass(mainly including Echinochloa crus-galli,Echinochloa oryzicola and Echinochloa colona)has a wide niche distribution and is extremely detrimental to agricultural production.In addition,the genus Echinochloa includes several domesticated species,called barnyard millet,with strong adaptability characteristics as orphan crops.Barnyard millet is an important grain resource under the background of climate changes.In this study,via de novo genome assembly and large-scale genome phenotyping and resequencing,multiple complex polyploid Echinochloa reference genomes and a global variation map of barnyard grass and millet are constructed.Systematical genomic studies on the Echinochloa speciation and evolution,global distribution of genetic polymorphisms for paddy barnyardgrass,genetic basis underlying important environmental adaptive traits and barnyard millet domestication,provide important insights and theoretical basis for basic biology of weeds,ecological weed control,and domestication and improvement of orphan crops.The main contents and conclusions are as follows:(1)Polyploidization in Echinochloa and comparison against wheat genomesDe novo genome assembly of hexaploid E.crus-galli,its diploid ancestor relative,Echinochloa haploclada,and its tetraploid ancestor,E.oryzicola,has been performed using the data generated by three-generation sequencing technology.The influences of polyploidization to environmental adaptation of barnyard grass are analyzed from the views of phylogeny,gene family and others.The main results are as follows:(a)The chromosome-level genome assembly of E.haploclada and the high-quality genome assemblies of E.oryzicola and E.crus-galli are obtained for the first time.(b)The hexaploidization of E.crus-galli genome occurred 310 thousand years ago,accompanied by the loss of disease resistance related genes such as NBS,possibly as a result of the "fitness cost",which is opposite to the wheat polyploidization process.(c)During the polyploidization of barnyard grass and wheat,the characteristics of subgenome selection pressure and gene expression dominance are different,which may be caused by the difference in selection type or intensity.(2)Global Echinochloa genomic diversity and barnyard millet domesticationUsing HiFi sequencing technology and a newly developed genome-scaffolding algorithm,the chromosome-level genome assembly of hexaploid E.colona is obtained,and the assemblies of E.crus-galli and E.oryzicola genomes are updated to be chromosome-level.Genome analyses have clarified the complex evolutionary process in the speciation of Echinochloa species.High-depth resequencing of 738 Echinochloa accessions around the world has been used to study the global Echinochloa genetic diversity,local environmental adaption,genetic mining of mechanisms underlying herbicide resistance and barnyard millet domestication.The main results are as follows:(a)The newly designed and developed allopolyploid genome scaffolding algorithm Dip Hi C has successfully mounted the genomes of hexaploid E.colona,hexaploid E.crus-galli and tetraploid E.oryzicola to chromosomes.(b)The reticulate evolution in Echinochloa genomes was caused by incomplete lineage sorting(ILS).(c)The global population structure of paddy barnyard grass was built,and the sympatric gene flow between hexaploid E.crus-galli and tetraploid E.oryzicola was detected.(d)Orthologous genes of Hd1 in both E.crus-galli and E.oryzicola genomes have undergone parallel selection in regulating flowering time.(e)High-quality reference genomes and population variation maps provide a basis for herbicide resistance interpretation.(f)The independent domestication of barnyard millet has led to the convergent evolution in morphology,and the key genes regulating plant architecture and grain shattering are subjected to parallel selection.(3)Genetic mechanism underlying crop mimicryThe phenomenon of barnyard grass imitating the erect plant architecture of rice in the seedling stage is called crop mimicry or Vavilov mimicry,which is one of the specific manifestations of environmental adaption for barnyard grass.Via genome sequencing and phenotyping of barnyard grass from paddy fields in the Yangtze River Basin,China,the genetic basis of crop mimicry was analyzed through population genomics.Results are as follows:(a)A mimicry index has been established to quantify the morphology similarity between barnyard grass and rice in paddy fields.(b)Genome differentiation between mimic and non-mimic barnyard grass population is observed and the genomes of mimic population are subject to unconscious positive selection by human agricultural production activities.(c)The key gene LA1 regulating plant architecture exhibits under parallel selection during crop mimicry and rice domestication.In conclusion,this study has generated multiple high-quality and complex Echinochloa reference genomes and a global variation atlas of barnyard grass and millet,through high-quality genome assembly,large-scale genome resequencing,and phenotyping,which provides new insights into the evolution,environmental adaptation,and domestication of orphan crops in Echinochloa.