An improved high-quality genome assembly and annotation of Tibetan hulless barley

Zeng, Xingquan; Xu, Tong; Ling, Zhihao; Wang, Yulin; Li, Xiangfeng; Xu, Shuqing; Xu, Qijun; Sang, Zha; Qimei, Wangmu; Basang, Yuzhen; Dunzhu, Jiabu; Yu, Mingzhai; Yuan, Hongjun; Tashi, Nyima

doi:10.1038/s41597-020-0480-0

Cited by 33 publications

(36 citation statements)

References 61 publications

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“…Interestingly, the barley nsLTP gene ( blt4 ) was also found in the cold stress response [ 27 , 28 ]. The latest physical, genetic and functional sequence assemblies of the barley and Qingke genomes were completed in 2012 and 2016 [ 29 , 30 ] and 2015, 2018, and 2020 [ 22 , 31 , 32 ], respectively, and they provided an important reference for future crop breeding, improvement, gene function and evolution research.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues

Duo

Xiong

et al. 2021

BMC Genomics

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Background Plant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant growth and development. To date, although the nsLTP gene family of barley (Hordeum vulgare L.) has been preliminarily identified, it is still unclear in the recently completed genome database of barley and Qingke, and its transcriptional profiling under abiotic stress has not been elucidated as well. Results We identified 40 barley nsLTP (HvLTP) genes through a strict screening strategy based on the latest barley genome and 35 Qingke nsLTP (HtLTP) orthologues using blastp, and these LTP genes were divided into four types (1, 2, D and G). At the same time, a comprehensive analysis of the physical and chemical characteristics, homology alignment, conserved motifs, gene structure and evolution of HvLTPs and HtLTPs further supported their similar nsLTP characteristics and classification. The genomic location of HvLTPs and HtLTPs showed that these genes were unevenly distributed, and obvious HvLTP and HtLTP gene clusters were found on the 7 chromosomes including six pairs of tandem repeats and one pair of segment repeats in the barley genome, indicating that these genes may be co-evolutionary and co-regulated. A spatial expression analysis showed that most HvLTPs and HtLTPs had different tissue-specific expression patterns. Moreover, the upstream cis-element analysis of HvLTPs and HtLTPs showed that there were many different stress-related transcriptional regulatory elements, and the expression pattern of HvLTPs and HtLTPs under abiotic stress also indicated that numerous HvLTP and HtLTP genes were related to the abiotic stress response. Taken together, these results may be due to the differences in promoters rather than by genes themselves resulting in different expression patterns under abiotic stress. Conclusion Due to a stringent screening and comprehensive analysis of the nsLTP gene family in barley and Qingke and its expression profile under abiotic stress, this study can be considered a useful source for the future studies of nsLTP genes in either barley or Qingke or for comparisons of different plant species.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues

Duo

Xiong

et al. 2021

BMC Genomics

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“…Analysis of the full length HvWRKY6 gene sequence from CI5791, Morex, and Tifang were identical ( Supplementary Figure 1 ) suggesting that the gene is conserved for its primary aa sequence across both resistant and susceptible barley genotypes. BLAST analysis of the barley pan-genome ( Jayakodi et al, 2020 ) showed 100% sequence identity for the lines Akashinriki, Barke, Golden Promise, Hockett, HOR 3081, HOR 3365, HOR 7552, HOR 8148, HOR 9043, HOR 10350, HOR 13821, HOR 13942, HOR 22559, Igri, OUN333, RGT Planet, ZDM02064 ( Jayakodi et al, 2020 ; Schreiber et al, 2020 ), Bowman ( IBGSC, 2012 ), Haruna Nijo ( Sato et al, 2016 ), and Lasa Goumang ( Zeng et al, 2020 ). Whereas, ZDM01467 ( Jayakodi et al, 2020 ) contained two concatenated hits of highly identical sequences suggesting a mis-assembly of the region.…”

Section: Resultsmentioning

confidence: 99%

The Barley HvWRKY6 Transcription Factor Is Required for Resistance Against Pyrenophora teres f. teres

et al. 2021

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Barley is an important cereal crop worldwide because of its use in the brewing and distilling industry. However, adequate supplies of quality malting barley are threatened by global climate change due to drought in some regions and excess precipitation in others, which facilitates epidemics caused by fungal pathogens. The disease net form net blotch caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt) has emerged as a global threat to barley production and diverse populations of Ptt have shown a capacity to overcome deployed genetic resistances. The barley line CI5791 exhibits remarkably effective resistance to diverse Ptt isolates from around the world that maps to two major QTL on chromosomes 3H and 6H. To identify genes involved in this effective resistance, CI5791 seed were γ-irradiated and two mutants, designated CI5791-γ3 and CI5791-γ8, with compromised Ptt resistance were identified from an M2 population. Phenotyping of CI5791-γ3 and -γ8 × Heartland F2 populations showed three resistant to one susceptible segregation ratios and CI5791-γ3 × -γ8 F1 individuals were susceptible, thus these independent mutants are in a single allelic gene. Thirty-four homozygous mutant (susceptible) CI5791-γ3 × Heartland F2 individuals, representing 68 recombinant gametes, were genotyped via PCR genotype by sequencing. The data were used for single marker regression mapping placing the mutation on chromosome 3H within an approximate 75 cM interval encompassing the 3H CI5791 resistance QTL. Sequencing of the mutants and wild-type (WT) CI5791 genomic DNA following exome capture identified independent mutations of the HvWRKY6 transcription factor located on chromosome 3H at ∼50.7 cM, within the genetically delimited region. Post transcriptional gene silencing of HvWRKY6 in barley line CI5791 resulted in Ptt susceptibility, confirming that it functions in NFNB resistance, validating it as the gene underlying the mutant phenotypes. Allele analysis and transcript regulation of HvWRKY6 from resistant and susceptible lines revealed sequence identity and upregulation upon pathogen challenge in all genotypes analyzed, suggesting a conserved transcription factor is involved in the defense against the necrotrophic pathogen. We hypothesize that HvWRKY6 functions as a conserved signaling component of defense mechanisms that restricts Ptt growth in barley.

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“…Each demultiplexed file was further mapped to a published reference of Hordeum vulgare (GenBank assembly accession: GCA_004114815.1 [55]) using BWA v.0.7.12-r1039 [56] with default settings, after first indexing the reference using the option '-a bwtsw' for a long reference genome. The aligned sam files were sorted by reference coordinates, and read groups were added into their headers with Picard tools.…”

Section: Snp Filteringmentioning

confidence: 99%

The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization

Xue

Greimler

Paun

et al. 2021

Biology

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The contrasting evolutionary histories of endemic versus related cosmopolitan species provide avenues to understand the spatial drivers and limitations of biodiversity. Here, we investigated the evolutionary history of three New Zealand endemic Deschampsia species, and how they are related to cosmopolitan D. cespitosa. We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the D. cespitosa populations of New Zealand, Australia and Korea. Whole plastid DNA analysis was performed on a larger worldwide sampling. Morphometrics of selected characters were applied to New Zealand sampling. Our RADseq review of over 55 Mbp showed the endemics as genetically well-defined from each other. Their last common ancestor with D. cespitosa lived during the last ten MY. The New Zealand D. cespitosa appears in a clade with Australian and Korean samples. Whole plastid DNA analysis revealed the endemics as members of a southern hemisphere clade, excluding the extant D. cespitosa of New Zealand. Both data provided strong evidence for hybridization between D. cespitosa and D. chapmanii. Our findings provide evidence for at least two migration events of the genus Deschampsia to New Zealand and hybridization between D. cespitosa and endemic taxa.

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An improved high-quality genome assembly and annotation of Tibetan hulless barley

Cited by 33 publications

References 61 publications

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues

The Barley HvWRKY6 Transcription Factor Is Required for Resistance Against Pyrenophora teres f. teres

The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization

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