A complete telomere-to-telomere assembly of the maize genome

Chen, Jian; Wang, Z; Tan, Kaiwen; Huang, Wei; Shi, Junpeng; Li, Tong; Hu, Jiang; Wang, Kai; Wang, Chao; Xin, Baoping; Zhao, Haiming; Song, Weibin; Schnable, James C.; Jin, Weiwei; Lai, Jinsheng

doi:10.1038/s41588-023-01419-6

Cited by 88 publications

(60 citation statements)

References 117 publications

(135 reference statements)

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“…The conservation of the CenH3 protein plays a pivotal role in determining the applicability of experimental methods for identifying centromeric regions in plants (Chen et al, 2023). The conservation of CenH3 proteins across various plant species was investigated by downloading protein sequences from NCBI and constructing a phylogenetic tree.…”

Section: Some Difficulties Exist In the Current Methods For Identifyi...mentioning

confidence: 99%

“…Centromere regions of A. thaliana, O. sativa (MH63RS3 and ZS97RS3) and Z. mays with T2T level genomes have been identified by experimental evidences (Chen et al, 2023;Naish et al, 2021;Song et al, 2021). Therefore, we selected them as the real datasets for testing the accuracy of CentIER.…”

Section: Validation Of Centier Accuracymentioning

confidence: 99%

“…In one scenario, TRs were not distributed in the centromeric region. For example, the absence of TRs was observed in chromosomes 5 and 8 of maize (Chen et al, 2023). In another scenario, TRs were present in the centromeric region, but the number of TRs was too low to distinguish the centromeric region from other repetitive regions in the chromosomes (such as telomeres).…”

Section: Potential Factors Affecting the Accuracy Of Centiermentioning

confidence: 99%

“…A. chinensis (Han et al, 2023), http://182.92.183.62/; C. limon (Bao et al, 2023), https://ngdc.cncb.ac.cn/search/?dbId=gwh&q=GWHCBFQ00000000.1; E. rufpilus (Wang et al, 2023), http://sugarcane.zhangjisenlab.cn/SugarcaneDB/#/downloads; O. sativa (Song et al, 2021), http://rice.hzau.edu.cn/cgi-bin/rice_rs3/download_ext; V. vinifera (Shi et al, 2023), https://zenodo.org/record/7751391#.ZBgVmcJBy3A; Z. mays (Chen et al, 2023), https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA751841.…”

Section: Dataset Download and Usage Of Toolsmentioning

confidence: 99%

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CentIER: accurate centromere identification for plant genomes with sequence specificity information

Xu,

Wen,

Feng

et al. 2023

Preprint

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Centromere identification is one of the important problems in genomics, providing a foundation for the studies of centromeres in aspects of composition, functionality, evolution, inheritance, and variation. The existing wet-experiment-based method is costly and time-consuming, while the bioinformatic method can only detect tandem repeats losing non-repetitive sequence regions in the centromere. To address these shortcomings, we introduce a new pipeline, CentIER, for the automatic and accurate identification and annotation of centromere regions by taking advantage of the sequence specificity information. CentIER only requires users to input the genomic sequence, and then it can partition the centromeric region from a chromosome, identify tandem repeat monomers, annotate retrotransposons, and ultimately output visualized results. By referencing the experimentally determined centromere regions, it was discovered that the predictive accuracy of centromere recognition by CentIER exceeded 90%. Following the evaluation of CentIER’s accuracy, it was applied to investigate the sequence and distribution characteristics of centromeric retrotransposons and tandem repeat sequences of different species, providing insights into these traits in monocotyledonous and dicotyledonous plants.

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Section: Some Difficulties Exist In the Current Methods For Identifyi...mentioning

confidence: 99%

Section: Validation Of Centier Accuracymentioning

confidence: 99%

Section: Potential Factors Affecting the Accuracy Of Centiermentioning

confidence: 99%

Section: Dataset Download and Usage Of Toolsmentioning

confidence: 99%

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CentIER: accurate centromere identification for plant genomes with sequence specificity information

Xu,

Wen,

Feng

et al. 2023

Preprint

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“…The utilization of long read technology, combined with Hi-C data for phasing, and advancement in assembly algorithms, enables the generation of telomere-to-telomere (T2T) gapless chromosome level assemblies (Zhou et al, 2022). In the last three years, researchers have assembled complete T2T genomes for several plant species, including arabidopsis (Wang et al, 2022), banana (Belser et al, 2021), barley (Navrátilová et al, 2022), maize (Chen et al, 2023), rice (Huang, 2023), soybean (Garg et al, 2023; Wang et al, 2023), and watermelon (Deng et al, 2022). These T2T genome assemblies have become the gold standard for the new era of genomics.…”

Section: Introductionmentioning

confidence: 99%

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Espina,

Lovell,

Jenkins

et al. 2024

Preprint

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Cultivar 'Williams 82' has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as 'Wm82-ISU-01' (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48,387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of 'Williams 82' reveal large regions of genomic heterogeneity, including regions of differential introgression from the genotype 'Kingwa' within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (~20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the 'Williams' haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of 'Williams 82'. In addition to the Wm82.a6 assembly, we also assembled the genome of soybean line 'Fiskeby III', a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with 'Fiskeby III' revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and 'Fiskeby III' genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

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Centromere diversity: How different repeat‐based holocentromeres may have evolved

Kuo,

Schubert,

Marques

et al. 2024

BioEssays

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In addition to monocentric eukaryotes, which have a single localized centromere on each chromosome, there are holocentric species, with extended repeat‐based or repeat‐less centromeres distributed over the entire chromosome length. At least two types of repeat‐based holocentromeres exist, one composed of many small repeat‐based centromere units (small unit‐type), and another one characterized by a few large centromere units (large unit‐type). We hypothesize that the transposable element‐mediated dispersal of hundreds of short satellite arrays formed the small centromere unit‐type holocentromere in Rhynchospora pubera. The large centromere unit‐type of the plant Chionographis japonica is likely a product of simultaneous DNA double‐strand breaks (DSBs), which initiated the de novo formation of repeat‐based holocentromeres via insertion of satellite DNA, derived from extra‐chromosomal circular DNAs (eccDNAs). The number of initial DSBs along the chromosomes must be higher than the number of centromere units since only a portion of the breaks will have incorporated eccDNA at an appropriate position to serve as future centromere unit sites. Subsequently, preferential incorporation of the centromeric histone H3 variant at these positions is assumed. The identification of repeat‐based holocentromeres across lineages will unveil the centromere plasticity and elucidate the mechanisms underlying the diverse formation of holocentromeres.

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A complete telomere-to-telomere assembly of the maize genome

Cited by 88 publications

References 117 publications

CentIER: accurate centromere identification for plant genomes with sequence specificity information

CentIER: accurate centromere identification for plant genomes with sequence specificity information

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Centromere diversity: How different repeat‐based holocentromeres may have evolved

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