The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution

Wei, Suyun; Yang, Yonghua; Yin, Tongming

doi:10.1038/s41438-020-0268-6

Cited by 42 publications

(34 citation statements)

References 63 publications

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“…Here, M. lutarioriparius (2 n = 2 x = 38) possesses a relatively large genome size with abundant repetitive sequences, which made it difficult to achieve a high-quality genome assembly using short-read sequencing technologies. Recently, the single-molecular, real-time sequencing technologies and high-throughput chromosome conformation capture (Hi-C) technology have been used in combination to make significant advances in the assembly of large and complicated plant genomes 11 .…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome

Miao

Feng

et al. 2021

Nat Commun

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Miscanthus, a rhizomatous perennial plant, has great potential for bioenergy production for its high biomass and stress tolerance. We report a chromosome-scale assembly of Miscanthus lutarioriparius genome by combining Oxford Nanopore sequencing and Hi-C technologies. The 2.07-Gb assembly covers 96.64% of the genome, with contig N50 of 1.71 Mb. The centromere and telomere sequences are assembled for all 19 chromosomes and chromosome 10, respectively. Allotetraploid origin of the M. lutarioriparius is confirmed using centromeric satellite repeats. The tetraploid genome structure and several chromosomal rearrangements relative to sorghum are clearly demonstrated. Tandem duplicate genes of M. lutarioriparius are functional enriched not only in terms related to stress response, but cell wall biosynthesis. Gene families related to disease resistance, cell wall biosynthesis and metal ion transport are greatly expanded and evolved. The expansion of these families may be an important genomic basis for the enhancement of remarkable traits of M. lutarioriparius.

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Section: Introductionmentioning

confidence: 99%

Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome

Miao

Feng

et al. 2021

Nat Commun

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“…Although Salix is the largest genus in the family Salicaceae sensu lato, with ~450 species (reviewed in He et al 2020), fewer Salix than Populus genomes have been assembled, and assemblies include only the cushion shrub S. brachista and the shrub willows S. purpurea, S. suchowensis, and S. viminalis (Chen et al 2019;Almeida et al 2020;Wei et al 2020;Zhou et al 2020). Shrub stature is a derived character, and the tree habit is ancestral , and is usual in poplars.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale assembly of the genome ofSalix dunniireveals a male-heterogametic sex determination system on chromosome 7

Jia

Zhang³

et al. 2020

Preprint

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Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 contigs, and includes 31,501 genes. We inferred a male heterogametic sex determining factor on chromosome 7, suggesting that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii X-linked region occupies about 3.21 Mb of chromosome 7, and is probably in a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for studying sex chromosome evolution in Salicaceae family.

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“…The repeat-masked genome was used for annotating gene models by combining the methods of homology-based, RNA-Seq-assisted, and ab initio predictions. With the homology-based prediction approach, protein sequences from the genome annotations of P. trichocarpa ( Tuskan et al 2006 ), P. simonii ( Wu et al 2020 ), Salix suchowensis ( Wei et al 2020 ), P. euphratica ( Zhang et al 2020 ), and P. deltiodes WV94 ( http://phytozome.jgi.doe.gov ) were collected and aligned against the genome using tBlastn (v2.2.31) ( Altschul et al 1997 ). The blast hits were refined for exact intron and exon positions using Exonerate (v2.4.0) ( Slater and Birney 2005 ).…”

Section: Methodsmentioning

confidence: 99%

Genome Assembly of SalicaceaePopulus deltoides(Eastern Cottonwood)I-69Based on Nanopore Sequencing and Hi-C Technologies

Bai

Zhang

et al. 2021

Journal of Heredity

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Populus deltoides is of significantly ecological and economic values, widely used in poplar breeding programs due to its superior characteristics such as rapid growth and resistance to disease. Although the genome sequence of P. deltoides WV94 is available, the assembly is fragmented. Here, we reported an improved chromosome-level assembly of the P. deltoides cultivar I-69 by combining Nanopore sequencing and chromosome conformation capture (Hi-C) technologies. The assembly was 429.3 Mb in size and contained 657 contigs with a contig N50 length of 2.62 Mb. Hi-C scaffolding of the contigs generated 19 chromosome-level sequences, which covered 97.4% (418 Mb) of the total assembly size. Moreover, repetitive sequences annotation showed that 39.28% of the P. deltoides genome was composed of interspersed elements, including retroelements (23.66%), DNA transposons (6.83%), and unclassified elements (8.79%). We also identified a total of 44,362 protein-coding genes in the current P. deltoides assembly. Compared with the previous genome assembly of P. deltoides WV94, the current assembly had some significantly improved qualities: the contig N50 increased 3.5-fold and the proportion of gaps decreased from 3.2% to 0.08%. This high-quality, well-annotated genome assembly provides a reliable genomic resource for identifying genome variants among individuals, mining candidate genes that control growth and wood quality traits, and facilitating further application of genomics-assisted breeding in populations related to P. deltoides.

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The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution

Cited by 42 publications

References 63 publications

Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome

Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome

Chromosome-scale assembly of the genome ofSalix dunniireveals a male-heterogametic sex determination system on chromosome 7

Genome Assembly of SalicaceaePopulus deltoides(Eastern Cottonwood)I-69Based on Nanopore Sequencing and Hi-C Technologies

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