Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields

Wang, Lifeng; Sun, Xuepeng; Peng, Yajun; Chen, Ke; Wu, Shan; Guo, Yanan; Zhang, Jingyuan; Yang, Haona; Jin, Tao; Wu, Lamei; Zhou, Xiaomao; Liang, Bin; Zhao, Zixiang; Liu, Ducai; Fei, Zhangjun; Bai, Lianyang

doi:10.1016/j.molp.2022.05.001

Cited by 21 publications

(31 citation statements)

References 73 publications

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“…Other studies reported homoeolog expression dominance in allopolyploid Brassica juncea (Yang et al., 2016), cotton ( Gossypium hirsutum ; Yoo et al., 2013) and switchgrass ( Panicum virgatum ; Lovell et al., 2021). In contrast, the absence of subgenome dominance has been observed in some recent polyploids, such as Capsella bursa‐pastoris , pear ( Pyrus bretschneideri ) and Chinese sprangletop ( Leptochloa chinensis ), and some ancient polyploids, such as soybean ( Glycine max ), banana ( Musa paradisiaca ), poplar ( Populus trichocarpa ) and Cucurbita (Douglas et al., 2015; Garsmeur et al., 2014; Li et al., 2019; Sun et al., 2017; Wang et al., 2022). Previous studies hypothesized that polyploidy without subgenome dominance may be autotetraploid (Garsmeur et al., 2014).…”

Section: Introductionmentioning

confidence: 99%

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

et al. 2023

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SUMMARY Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops, and is a valuable resource to secure food diversity and combat drought stresses under the global warming scenario. However, due to the absence of extant diploid progenitors, the polyploidy genome of broomcorn millet remains poorly understood. Here, we report the chromosome‐scale genome assembly of broomcorn millet. We divided the broomcorn millet genome into two subgenomes using the genome sequence of Panicum hallii, a diploid relative of broomcorn millet. Our analyses revealed that the two subgenomes diverged at ~4.8 million years ago (Mya), while the allotetraploidization of broomcorn millet may have occurred about ~0.48 Mya, suggesting that broomcorn millet is a relatively recent allotetraploid. Comparative analyses showed that subgenome B was larger than subgenome A in size, which was caused by the biased accumulation of long terminal repeat retrotransposons in the progenitor of subgenome B before polyploidization. Notably, the accumulation of biased mutations in the transposable element‐rich subgenome B led to more gene losses. Although no significant dominance of either subgenome was observed in the expression profiles of broomcorn millet, we found the minimally expressed genes in P. hallii tended to be lost during diploidization of broomcorn millet. These results suggest that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels.

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Section: Introductionmentioning

confidence: 99%

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

et al. 2023

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“…The ancestor of O. kokonorica and C. songorica diverged from O. thomaeum˜20.86 Ma, which together diverged from E. tef ˜26.19 Ma (Figure 2A). The phylogenetic relationships among these 16 species were the same as those recovered from previous studies (Wang et al, 2022).…”

Section: Comparative Genomic and Phylogenetic Analysismentioning

confidence: 62%

“…kokonorica and C. songorica are both tetraploids belonging to the same subtribe of Chloridoideae, and C. songoricahas been revealed to be an allotetraploid species with 20 chromosomes assigned to two subgenomes (Zhang et al, 2021a). Therefore, we partitioned the O. kokonorica genome into subgenomes A and B by dotplot with syntenic blocks and synonymous nucleotide substitutions (K s) values against the C. songorica subgenomes using WGDI (Sun et al, 2022). Analysis of homoeolog expression bias was preformed following VanBuren et al (2020) for all five tissues and samples under three abiotic treatments (see below).…”

Section: Genome Synteny K S Analysis Subgenome Identification and Hom...mentioning

confidence: 99%

Comparative genomics provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Qu¹,

Ai²,

Yin

et al. 2023

Preprint

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Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale reference genome assembly for the genus Orinus (Orinus kokonorica as representative) and preformed comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and their two subgenomes display neither fractionation bias nor global homoeolog expression dominance. Recent expansion of transposable elements and enormous contraction in gene families in O. kokonorica have maintained a similar genome size compared to C. songorica. Further comparative genomic analyses reveal substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations in flower and rhizome development related genes and extensive SVs between orthologs may contribute to the morphological differences between the two genera. Our results provide significant new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.

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“…The genome of weedy rice (Oryza sativa f. spontanea) was also sequenced and assembled, at the chromosome level, in 2019 (Sun et al 2019). In addition, the genomes of tetraploid Chinese sprangletop (Leptochloa chinensis) were assembled (Wang et al 2022). An invasive weed in wheat fields, field pennycress (Thlaspi arvense), had its genome assembled in 2015 and independently anchored to chromosomes in 2021 and 2022 (Dorn et al 2015;Geng et al 2021;Nunn et al 2022).…”

Section: Weed Genome Sequencing and De Novo Assemblymentioning

confidence: 99%

Weed genomics: yielding insights into the genetics of weedy traits for crop improvement

Huang

et al. 2023

aBIOTECH

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Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (Barbarea vulgaris) to almost 4.4 Gb (Aegilops tauschii). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.

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Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields

Cited by 21 publications

References 73 publications

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

Comparative genomics provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Weed genomics: yielding insights into the genetics of weedy traits for crop improvement

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