Chromosome-scale assembly of the bread wheat genome, Triticum aestivum, reveals over 5700 new genes

ABSTRACTBread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all 3 wheat subgenomes at chromosome scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 gigabases of genomic sequence. We earlier published an independent wheat assembly (Triticum 3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC 1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum 4.0, contains 15.07 gigabases of non-gap sequence anchored to chromosomes, which is 1.2 gigabases more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered more than 5700 new genes, all of them duplications in the Chinese Spring genome that are missing from the IWGSC assembly and annotation. The Triticum 4.0 assembly and annotations are freely available at www.ncbi.nlm.nih.gov/bioproject/PRJNA392179.

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Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies

Genetics ◽

10.1534/genetics.120.303501 ◽

2020 ◽

Vol 216 (2) ◽

pp. 599-608 ◽

Cited By ~ 3

Author(s):

Michael Alonge ◽

Alaina Shumate ◽

Daniela Puiu ◽

Aleksey V. Zimin ◽

Steven L. Salzberg

Keyword(s):

Bread Wheat ◽

Chinese Spring ◽

Genomic Sequence ◽

Chromosome Length ◽

Photoperiod Response ◽

Additional Gene ◽

Reference Assembly ◽

Genetics Research ◽

Gene Copies ◽

Bread Wheat Genome

Bread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC CS v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all three wheat subgenomes at chromosome-scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 Gbp of genomic sequence. We earlier published an independent wheat assembly (Triticum_aestivum_3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC CS v1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum_aestivum_4.0, contains 15.07 Gbp of nongap sequence anchored to chromosomes, which is 1.2 Gbps more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered >5700 additional gene copies, facilitating the accurate annotation of functional gene duplications including at the Ppd-B1 photoperiod response locus.

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Extensive Pericentric Rearrangements in the Bread Wheat ( Triticum aestivum L.) Genotype “Chinese Spring” Revealed from Chromosome Shotgun Sequence Data

Genome Biology and Evolution ◽

10.1093/gbe/evu237 ◽

2014 ◽

Vol 6 (11) ◽

pp. 3039-3048 ◽

Cited By ~ 21

Author(s):

Jian Ma ◽

Jiri Stiller ◽

Yuming Wei ◽

You-Liang Zheng ◽

Katrien M. Devos ◽

...

Keyword(s):

Triticum Aestivum ◽

Bread Wheat ◽

Chinese Spring ◽

Sequence Data ◽

Triticum Aestivum L ◽

Shotgun Sequence

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The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

GigaScience ◽

10.1093/gigascience/gix097 ◽

2017 ◽

Vol 6 (11) ◽

Cited By ~ 96

Author(s):

Aleksey V Zimin ◽

Daniela Puiu ◽

Richard Hall ◽

Sarah Kingan ◽

Bernardo J Clavijo ◽

...

Keyword(s):

Triticum Aestivum ◽

Bread Wheat ◽

Wheat Genome ◽

Bread Wheat Genome

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Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly

The Plant Journal ◽

10.1111/tpj.15289 ◽

2021 ◽

Author(s):

Tingting Zhu ◽

Le Wang ◽

Hélène Rimbert ◽

Juan C. Rodriguez ◽

Karin R. Deal ◽

...

Keyword(s):

Triticum Aestivum ◽

Bread Wheat ◽

Genome Assembly ◽

Chinese Spring ◽

Optical Maps

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Aneuhaploids in bread wheat

Genetics Research ◽

10.1017/s0016672300016700 ◽

1976 ◽

Vol 28 (1) ◽

pp. 37-45 ◽

Cited By ~ 24

Author(s):

T. E. Miller ◽

Victor Chapman

Keyword(s):

Triticum Aestivum ◽

Genetic Control ◽

Bread Wheat ◽

Chromosome Pairing ◽

Chinese Spring ◽

Meiotic Chromosome ◽

Hordeum Bulbosum ◽

Meiotic Abnormalities ◽

Meiotic Chromosome Pairing

SUMMARYEuploid and aneuploid plants of Triticum aestivum, variety Chinese Spring were pollinated with, pollen of Hordeum bulbosum. Euhaploids and aneuhaploids of Chinese Spring were obtained from the crosses. Meiotic chromosome pairing was analysed in 25 different aneuhaploids and the results were compared with those obtained from euhaploids. The evidence provided by the meiotic studies was used to identify chromosomes whose activities affected the genetic control of chromosome pairing.Meiosis was abnormal in a 23-chromosome aneuhaploid and in the 22-chromosome sectors of a chimaeral plant. Both plants were thought to have resulted from the incomplete elimination of the genome of H. bulbosum from hybrid embryos. It is suggested that the meiotic abnormalities in the two aneuhaploids were caused by the residual barley chromosomes.

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The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

10.1101/159111 ◽

2017 ◽

Cited By ~ 5

Author(s):

Aleksey V. Zimin ◽

Daniela Puiu ◽

Richard Hall ◽

Sarah Kingan ◽

Bernardo J. Clavijo ◽

...

Keyword(s):

Triticum Aestivum ◽

Bread Wheat ◽

Aegilops Tauschii ◽

Weighted Average ◽

Wheat Genome ◽

D Genome ◽

Genetic Studies ◽

Final Assembly ◽

Bread Wheat Genome ◽

Diploid Ancestor

AbstractCommon bread wheat, Triticum aestivum, has one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall size of more than 15 billion bases. Multiple past attempts to assemble the genome have failed. Here we report the first successful assembly of T. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads. The final assembly contains 15,344,693,583 bases and has a weighted average (N50) contig size of of 232,659 bases. This represents by far the most complete and contiguous assembly of the wheat genome to date, providing a strong foundation for future genetic studies of this important food crop. We also report how we used the recently published genome of Aegilops tauschii, the diploid ancestor of the wheat D genome, to identify 4,179,762,575 bp of T. aestivum that correspond to its D genome components.

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Suppression of rust resistance in bread wheat (Triticum aestivum L.) by D-genome chromosomes

Genome ◽

10.1139/g92-043 ◽

1992 ◽

Vol 35 (2) ◽

pp. 276-282 ◽

Cited By ~ 54

Author(s):

D. Bai ◽

D. R. Knott

Keyword(s):

Triticum Aestivum ◽

Leaf Rust ◽

Bread Wheat ◽

Stem Rust ◽

Chinese Spring ◽

Rust Resistance ◽

Leaf Rust Resistance ◽

Triticum Aestivum L ◽

D Genome ◽

Or Genes

Several tests were done in bread wheat (Triticum aestivum L.) to demonstrate the occurrence of genes on D-genome chromosomes that suppress resistance to leaf rust (Puccinia recondita f. sp. tritici Rob. ex Desm.) and stem rust (Puccinia graminis f. sp. tritici Eriks. &Henn.). Ten rust-resistant wild tetraploid wheats (T. turgidum var. dicoccoides) were crossed with both durum (T. turgidum var. durum) and bread wheats. In all cases, resistance to leaf rust and stem rust was expressed in the hybrids with durum wheats but suppressed in the hybrids with bread wheats. Crosses were made between five diverse durum wheats and four diverse bread wheats. The pentaploid hybrid seedlings of 12 crosses were tested with leaf rust race 15 and in all cases the resistance of the durum parents was suppressed. Fourteen D-genome disomic chromosome substitution lines in the durum wheat 'Langdon' were tested with stem rust race 15B-1 and leaf rust race 15. Chromosomes 1B, 2B, and 7B were found to carry genes for resistance to stem rust but no suppressors were detected. Chromosomes 2B and 4B carried genes for resistance to leaf rust, and 1D and 3D carried suppressors. Crosses between seven D-genome monosomies of 'Chinese Spring' and three dicoccoides accessions showed that 'Chinese Spring' possesses genes on 1D, 2D, and 4D, which suppress the stem rust resistance of all three dicoccoides accessions. All three chromosomes must be present to suppress resistance, indicating that some form of complementary gene interaction is involved. In addition, 'Chinese Spring' carries a gene or genes on 3D that suppresses the leaf rust resistance of all three dicoccoides accessions, plus a gene or genes on 1D that suppresses the leaf rust resistance of only one of them. The data raise some interesting questions about the specificity of the suppressors. The high frequency of occurrence of suppressors in the bread wheat population suggests that they must have a selective advantage.Key words: Triticum aestivum, stem rust, leaf rust, rust resistance, suppressor.

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