2020
DOI: 10.1038/s41438-020-0268-6
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The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution

Abstract: Salix suchowensis is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of S. suchowensis was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of S. suchowensis generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was~65-fold higher than that reported prev… Show more

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Cited by 42 publications
(34 citation statements)
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References 63 publications
(70 reference statements)
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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%
“…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%
“…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%
“…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%