The chromosome-based genome provides insights into the evolution in water spinach

Hao, Yuanyuan; Bao, Wenjing; Li, Guoli; Gagoshidze, Zakaria; Shu, Huangying; Yang, Zifeng; Cheng, Shanhan; Zhu, Guopeng; Wang, Zhiwei

doi:10.1016/j.scienta.2021.110501

Cited by 16 publications

(21 citation statements)

References 30 publications

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“…However, little is known about the MYB gene family in I. aquatica and its expression patterns in response to Cd stress due to a lack of genomic information. In our previous work, we constructed a high-quality chromosome-level genome assembly of I. aquatica (Hao et al, 2021), which provides excellent sequence resources for comprehensive analysis of the MYB gene family in I. aquatica. In the present study, we performed genome-wide identification of IaMYB genes by conducting the bioinformatic search of I. aquatica genome and analyzed their sequence features, gene duplication modes, selective pressure, expression patterns under Cd stress, and cis-acting elements.…”

Section: Introductionmentioning

confidence: 99%

“…Ipomoea aquatica is one of the only two edible plants in the family Convolvulaceae, which is widely distributed in tropical and subtropical areas ( Hao et al, 2021 ). The characteristic of the high capacity of Cd accumulation together with strong adaptability to Cd stress brought I. aquatica into focus for studying plant response to Cd stress ( Wang et al, 2007 ; Shen et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification of myeloblastosis gene family and its response to cadmium stress in Ipomoea aquatica

et al. 2022

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The myeloblastosis (MYB) proteins perform key functions in mediating cadmium (Cd) tolerance of plants. Ipomoea aquatica has strong adaptability to Cd Stress, while the roles of the I. aquatica MYB gene family with respect to Cd stress are still unclear. Here, we identified a total of 183 MYB genes in the I. aquatica genome (laMYB), which were classified into 66 1R-type IaMYB, 112 2R-type IaMYB, four 3R-type IaMYB, and one 4R-type IaMYB based on the number of the MYB repeat in each gene. The analysis of phylogenetic tree indicated that most of IaMYB genes are associated with the diverse biological processes including defense, development and metabolism. Analysis of sequence features showed that the IaMYB genes within identical subfamily have the similar patterns of the motif distributions and gene structures. Analysis of gene duplication events revealed that the dispersed duplication (DSD) and whole-genome duplication (WGD) modes play vital roles in the expansion of the IaMYB gene family. Expression profiling manifests that approximately 20% of IaMYB genes had significant role in the roots of I. aquatica under Cd stress. Promoter profiling implied that the differentially expressed genes might be induced by environmental factors or inherent hormones and thereby execute their function in Cd response. Remarkably, the 2R-type IaMYB157 with abundant light-responsive element G-box and ABA-responsive element ABRE in its promoter region exhibited very strong response to Cd stress. Taken together, our findings provide an important candidate IaMYB gene for further deciphering the molecular regulatory mechanism in plant with respect to Cd stress.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of myeloblastosis gene family and its response to cadmium stress in Ipomoea aquatica

et al. 2022

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“…The TE-masked genome was used for protein-coding gene prediction by using Augustus v3.4.0 ( Stanke et al 2006 ), with transcript and homology hints and parameter “–softmasking=on.” The full-length transcript hints were generated by mapping RNA sequences from PacBio Iso-Seq sequencing to the genome with GMAP v2020-10-27 ( Wu and Watanabe 2005 ), removing the hints with identity <0.95 or coverage <0.95, and transforming to hints by blat2hints.pl in Augustus. The homology hints were generated by aligning the protein-coding sequences from the published genome for the species of I. aquatica ( Hao et al 2021 ), Ipomoea nil ( Hoshino et al 2016 ), I. trifida , and I. triloba ( Wu et al 2018 ) to the genome assembly, using Exonerate v2.2.0 ( Slater and Birney 2005 ) with parameter “–% 70,” and transforming to hints by exonerate2hints.pl in Augustus. The training parameters of Augustus were generated during the BUSCO ( Simao et al 2015 ) completeness assessment of the assembled contigs with parameter “–augustus” and applied here.…”

Section: Methodsmentioning

confidence: 99%

“…The genome data of I. cairica , 9 well-assembled species in order Solanales [ I. aquatica ( Hao et al 2021 ), I. nil ( Hoshino et al 2016 ), I. trifida , I. triloba ( Wu et al 2018 ), Cuscuta australis ( Sun et al 2018 ), C uscuta campestris ( Vogel et al 2018 ), Solanum lycopersicum ( Mueller et al 2009 ), Solanum tuberosum ( Xu et al 2011 ; Pham et al 2020 ), and Capsicum annuum ( Kim et al 2014 )), and Coffea canephora ( Denoeud et al 2014 )], were compared. The orthologous groups (orthogroups) were built for these species using OrthoFinder v2.5.2 ( Emms and Kelly 2019 ) with parameter “-M msa -A mafft -T fasttree -l -y.” To infer the phylogeny relationship of these species, the protein sequences of single-copy orthogroups were separately aligned using MUSCLE v3.8.1551 ( Edgar 2004 ) and then concatenated into 1 super sequence for each species.…”

Section: Methodsmentioning

confidence: 99%

“…However, these 2 genome assemblies were still fragmented (with the longest contig N50 size of 65.8 kb), due to the constrains in the sequencing and assembly technologies ( Wu et al 2018 ). In addition, a chromosome-level genome assembly of Ipomoea aquatica was generated recently, which made a great improvement in assembly continuity with contig N50 sizes of 1.7 Mb ( Hao et al 2021 ), but still far from some recently published genomes ( Liu et al 2022 ; Lu et al 2022 ). In this study, we present a high-quality chromosome-level genome for diploid species of I. cairica (2 n = 2 x = 30) by using Pacific Biosciences (PacBio) HiFi and Hi-C sequencing data.…”

Section: Introductionmentioning

confidence: 99%

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A chromosome-level reference genome of a Convolvulaceae species Ipomoea cairica

Jiang

Wang

et al. 2022

G3 Genes|Genomes|Genetics

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Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by PacBio HiFi and Hi-C sequencing, with assembly size of 733.0 Mb, contig N50 of 43.8 Mb and scaffold N50 of 45.7 Mb, and BUSCO complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere-to-telomere. The transposable element content of I. cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the BUSCO complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that I. cairica formed a clade with I. aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of I. cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness.

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The Future of Crop Improvement in Sweetpotato: Merging Traditional and Genomic-Assisted Breeding Methods

Oloka,

da Silva,

Azevedo

et al. 2024

Compendium of Plant Genomes

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Crop improvement in sweetpotato has progressed slowly in many parts of the world largely due to its significant genetic complexity arising from its large autohexaploid genome, high heterozygosity, and self and cross-incompatibilities. New breeding tools have been developed to better understand this crop and its important agronomic and culinary traits. These tools and their application are reviewed here, and the path forward has been proposed. By incorporating these new genomic tools into breeding programs routinely alongside the traditional methods, crop improvement can be accelerated, leading to the delivery of clones with better genetics to farmers more quickly. This integration of genomics could propel sweetpotato into a new era, ultimately enhancing its productivity and profitability, which is crucial given the growing global population.

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The chromosome-based genome provides insights into the evolution in water spinach

Cited by 16 publications

References 30 publications

Genome-wide identification of myeloblastosis gene family and its response to cadmium stress in Ipomoea aquatica

Genome-wide identification of myeloblastosis gene family and its response to cadmium stress in Ipomoea aquatica

A chromosome-level reference genome of a Convolvulaceae species Ipomoea cairica

The Future of Crop Improvement in Sweetpotato: Merging Traditional and Genomic-Assisted Breeding Methods

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