De novo assembly of a Chinese soybean genome

Shen, Yanting; Liu, Jing; Geng, Hui-Xia; Zhang, Jixiang; Liu, Yucheng; Zhang, Haikuan; Xing, Shilai; Du, Jing; Ma, Shisong; Tian, Zhixi

doi:10.1007/s11427-018-9360-0

Cited by 133 publications

(87 citation statements)

References 104 publications

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“…A second assembly, Wm82.a2, was released by DOE‐JGI in 2014 and comprised 949 Mbp in 20 pseudomolecules, plus 29.3 Mbp in 1170 unanchored scaffolds (Song et al ., ). Additional ab initio (Salamov and Solovyev, ) soybean genome assemblies have been released recently: Zhonghuang 13 (Shen et al ., ); Enrei (Shimomura et al ., ); a perennial relative of soybean, Glycine latifolia (Liu et al ., ); draft assemblies for seven wild soybean accessions (Li et al ., ); and a high‐quality G. soja assembly for accession W05 (Xie et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Construction and comparison of three reference‐quality genome assemblies for soybean

et al. 2019

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We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

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Section: Introductionmentioning

confidence: 99%

Construction and comparison of three reference‐quality genome assemblies for soybean

et al. 2019

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“…This different numbers might be not only correlated with the size of plant genomes but also related to gene duplication. The genomes of Arabidopsis thaliana (125Mb, 25498 protein coding genes) [71], potato (844Mb, 39031) [72], poplar (385Mb, 45555) [73], Asian pears (527Mb, 59552) [74] and soybean (1.025 Gb, 52051) [75] are smaller than that of moso bamboo and the total number of protein-coding genes varies widely. On one hand, potato has experienced two rounds of whole-genome triplication events (WGT) [72]; Arabidopsis thaliana and soybean have undergone three genome duplication events, including two doublings and one triple [76]; in Populus, apart from a triploid event, there is a single "salicoid" duplication event (P-duplication) [73]; Asian pears is similar to poplar, with one doubling and one triple [59].…”

Section: Evolutionary Relationshipsmentioning

confidence: 99%

Systematic Identification and Analysis of NAC Gene Family in Moso Bamboo (Phyllostachys edulis)

Gao¹,

Liu²,

Wu³

et al. 2020

Preprint

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Background: NAC (NAM/ATAF1/2/CUC2) gene family is a large plant-specific transcription factor family, which is implicated in many functions, such as morphogenesis, the thickness formation of secondary cell walls as well as biotic and abiotic stress and more. In moso bamboo ( Phyllostachys edulis ), 94 PeNACs have been identified and three members are predicted to relate to the secondary cell wall. However, there were few studies on moso bamboo NAC genes under stress.Results: In this study, we re-identified 165 PheNACs with the latest moso bamboo genome data and divided them into 12 subfamilies using NAM domains. Gene structure and motif distribution manifested the NAC gene family was fairly conserved. Evolutionary analysis showed that the segmental duplication played a significant role in the expansion of NAC genes and the relationship between moso bamboo and Brachypodium distachyon was closest than beween moso bamboo and other four species ( Arabidopsis thaliana, Oryza sativa , Sorghum bicolor and Zea mays ). Based on the promoter analysis of the 27 NAC members in A subfamily, quantitative real-time PCR exhibited these genes reacted differently under drought, high salt, abscisic acid and methyl jasmonate treatments. Finally, we selected out four potential stress-associated genes (PheNAC001, -056, -080 and -100) and found they all localized in the tobacco nucleus and had transcriptional activity in yeast.Conclusions: These preliminary results provide valuable information for mining potential resistance NAC genes and lay theoretical basis for breeding new stress-resistant varieties in moso bamboo.

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“…The genome accuracy rate was evaluated as 99.999% by using resequencing data and GATK tools [13,14] (See methods). BUSCO score of the assembly was 93.2% [15] (Table 2), indicating that the completeness of JD17 was higher than that of the Wm82, ZH13, and W05 genomes [16,17]. Table 1 Assembly statistics of Glycine_max_JD17 (JD17), Glycine_max_v2.0 (Wm82), Gmax_ZH13 (ZH13) and W05.…”

Section: Construction Of a Platinum-grade Soybean Reference Genomementioning

confidence: 99%

Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits

Yi¹,

Liu²,

Chen³

et al. 2020

Preprint

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BackgroundCultivated soybean (Glycine max) is an important source for protein and oil. Each soybean strain has its own genetic diversity, and the availability of more soybean genomes may enhance comparative genomic analysis of soybean.ResultsIn this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with high contiguity, completeness, and accuracy. We annotated 59,629 gene models and reconstructed 235,109 high-quality full-length transcripts. We have molecularly characterized the genotypes of some important agronomic traits of JD17 by taking advantage of these newly established genomic resources.ConclusionsWe reported a high-quality genome and annotations of a wide range of cultivars, and used them to analyze the genotypes of genes related to important agronomic traits of soybean in JD17. We have demonstrated that high-quality genome assembly can serve as a valuable reference for soybean genomics and breeding research community.

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De novo assembly of a Chinese soybean genome

Cited by 133 publications

References 104 publications

Construction and comparison of three reference‐quality genome assemblies for soybean

Construction and comparison of three reference‐quality genome assemblies for soybean

Systematic Identification and Analysis of NAC Gene Family in Moso Bamboo (Phyllostachys edulis)

Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits

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