<i>De novo</i> genome assembly of the red silk cotton tree (<i>Bombax ceiba</i>)

Gao, Yong; Wang, Haibo; Liu, Chao; Chu, Honglong; Dai, Dong-Qin; Song, Shengnan; Yu, Liang; Han, Lihong; Fu, Yi; Tian, Bin; Tang, Lizhou

doi:10.1093/gigascience/giy051

Cited by 35 publications

(23 citation statements)

References 44 publications

(54 reference statements)

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“…The Ks approach identified a Ks peak in most species, corroborating prior analyses (Paterson et al ; Chen et al ; Kim et al ; Teh et al ; Gao et al ). While the modes of these distributions differ between species, the full distributions overlap markedly among species, and also overlap with speciation estimates.…”

Section: Discussionsupporting

confidence: 83%

“…To complement already published genome and transcriptome data (see Methods and Supplemental Table S1 for summary of taxa sampled and references), we generated transcriptomes for Tilia cordata (Tilioideae), Adansonia digitata (Bombacoideae), and Bombax ceiba (Bombacoideae), although the Bombax transcriptome was superseded by the recent publication of a genome sequence for Bombax ceiba (Gao et al ). Raw data for these three transcriptomes are available on NCBI Sequence Read Archive, under accession PRJNA493960.…”

Section: Resultsmentioning

confidence: 99%

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A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Conover

Karimi

Stenz

et al. 2019

JIPB

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Previous research suggests that Gossypium has undergone a 5‐ to 6‐fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae‐Bombacoideae and Sterculioideae‐Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae‐Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

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Section: Discussionsupporting

confidence: 83%

Section: Resultsmentioning

confidence: 99%

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Conover

Karimi

Stenz

et al. 2019

JIPB

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“…With respect to a previously reported SGS-based assembly of the American barn swallow genome using a comparable amount of raw data [2], even the contigs generated from long-read sequencing alone show a 134-fold increase in N50, similar to the increase recently obtained for the Anna's hummingbird genome using the same technologies [15]. Furthermore, the 1.6 fold change in scaffold N50 attained by Bionano NLRS hybrid scaffolding before removal of haplotigs is comparable with results obtained by other genome assemblies that have employed this method [58]. Strikingly, the new DLS method greatly outperformed the NLRS system, providing a 3.3 fold increase of N50 (before removal of haplotigs).…”

Section: Resultssupporting

confidence: 83%

SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)

Formenti

Chiara

Poveda

et al. 2018

Preprint

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BackgroundThe barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference genome assembly for the European subspecies (H. r. rustica).FindingsAs part of the Genome10K (G10K) effort on generating high quality vertebrate genomes, we have assembled a highly contiguous genome assembly using Single Molecule Real-Time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived both from the Nick, Label, Repair and Stain and from the Direct Label and Stain (DLS) technologies. As proposed by Bionano, the DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of over 25.95 Mbp.ConclusionsThis high-quality genome assembly represents a valuable resource for further studies of population genetics and genomics in the barn swallow, and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.

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“…Genome expansions and evolution. Among genome-sequenced plants of the order Malvales [27][28][29][30] , D 5 and the D t1 -subgenome in (AD) 1 are similar in genome sizes relative to Bombax ceiba or Durio zibethinus, but are expanded nearly twofold compared with the Theobroma cacao and Corchorus capsularis genomes (Fig. 4a).…”

Section: Chromosomal Translocation and Inversions Within Gossypiummentioning

confidence: 99%

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

et al. 2020

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ultivated cotton is one of the most economically important crop plants in the world. The allotetraploid Upland cotton, G. hirsutum (n = 2x = 26, (AD) 1), currently dominates the world's cotton commerce 1,2. Hybridization between the Old World A-genome progenitor and a New World D-genome ancestor, followed by chromosome doubling, formed the allopolyploid cotton ~1−2 million years ago (Ma) 3,4. Uncertainty regarding the actual A-genome donor of the widely cultivated allotetraploid cotton G. hirsutum has persisted 5-13. A 1 (n = x = 13) and A 2 (n = x = 13), commonly known as African and Asiatic cotton, respectively, are the only two extant diploid A-genome species in the world 14. Stephens first proposed in Nature, using genetic and morphological evidence, that A 2 was the A-genome donor of present-day allopolyploid cottons 6. Gerstel argued via cytogenetic studies that A 1 was more closely related to the A-genome in the allopolyploids than A 2 (ref. 8). Despite recent efforts to sequence the cotton genomes, including Gossypium raimondii (D 5) 15,16 , A 2 (refs. 17,18), (AD) 1 (refs. 10,19-21) and Gossypium barbadense 10,21 ((AD) 2 , a much less cultivated tetraploid cotton), the origin history of the A-genome donor for the tetraploid (AD) 1-genome 5,11,13 and the extent of divergence between the A-genomes remain elusive 22,23. Abundant studies support a Gossypium species resembling D 5 as the D-genome donor 13 , but currently there is no solid evidence to suggest that the actual A-genome donor of tetraploid cottons is either A 2 (refs. 6,7,10,19) or A 1 (refs. 8,9,11-13) as has been suggested. In this study, we assembled A 1 variety africanum for the first time and reassembled high-quality A 2 cultivar Shixiya1 and (AD) 1 genetic standard Texas Marker-1 (TM-1) genomes on the basis of PacBio long reads, paired-end sequencing and high-throughput chromosome conformation capture (Hi-C) technologies. Upon assembling and updating cotton genomes, we revealed the origin of cotton A-genomes, the occurrence of several transposable element (TE) bursts and the genetic divergence of diploid A-genomes worldwide. Also, we identified abundant structural variations (SVs) that have affected the expression of neighboring genes and help explain phenotypic differences among the cotton species. Results Sequencing and assembly of three high-quality cotton genomes. Here we sequenced the A 1-genome var. africanum for the first time by generating ~225-gigabase (Gb) PacBio single-molecule real-time (SMRT) long reads (the N50 (minimum length to cover 50% of the total length) of these reads was 13 kilobases (kb)) with 138-fold genome coverage. We generated an assembly that captured 1,556 megabases (Mb) of genome sequences, consisting of 1,781 contigs with the N50 of these contigs reaching up to 1,915 kb (Table 1). The initial assemblies were then corrected by using highly accurate Illumina paired-end reads (Supplementary Table 1). Finally, 95.69% of total contigs spanning 1,489 Mb were categorized and ordered into 13 chromosome-scale scaffold...

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De novo genome assembly of the red silk cotton tree (Bombax ceiba)

Cited by 35 publications

References 44 publications

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

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