De novo assemblies of <i>Luffa acutangula</i> and <i>Luffa cylindrica</i> genomes reveal an expansion associated with substantial accumulation of transposable elements

Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat; Nawae, Wanapinun; Yoocha, Thippawan; Kongkachana, Wasitthee; Sangsrakru, Duangjai; Jomchai, Nukoon; U‐thoomporn, Sonicha; Sheedy, John Robert; Buaboocha, Jarunee; Mekiyanon, Supat; Tangphatsornruang, Sithichoke

doi:10.1111/1755-0998.13240

Cited by 27 publications

(23 citation statements)

References 80 publications

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“…L. acutangula has an estimated genome size of 760 Mb, spread over 13 chromosomes. It has approximately 42,211 predicted gene models, of which 32,233 are protein-coding genes with an average gene size of 2886 nt 22 . The 112 L. acutangula accessions of this study originated from two genetic resources.…”

Section: Resultsmentioning

confidence: 99%

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Perez

Tongyoo

Chunwongse

et al. 2021

Sci Rep

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This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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Section: Resultsmentioning

confidence: 99%

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Perez

Tongyoo

Chunwongse

et al. 2021

Sci Rep

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“…Leaf tissues from one mature B. sexangula individual located in the natural mangrove forest under the protection of the Department of Marine and Coastal Resources (Ranong Province; 10°10′15.45″N 98°42′26.89″E) were collected, immediately frozen, and stored in liquid nitrogen until use. High-molecular weight genomic DNA was extracted and evaluated following the protocol in Pootakham, Sonthirod, et al (2021 ). For transcriptome sequencing, we isolated total RNA from leaf tissues collected from the same individual used for genome sequencing following the protocol in Pootakham, Nawae, et al (2021 ).…”

Section: Methodsmentioning

confidence: 99%

De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome

Pootakham

Naktang

Sonthirod

et al. 2022

Genome Biology and Evolution

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Upriver orange mangrove (Bruguiera sexangula) is a member of the most mangrove-rich taxon (Rhizophoraceae family) and is commonly distributed in the intertidal zones in tropical and subtropical latitudes. In this study, we employed the 10x Genomics linked-read technology to obtain a preliminary de novo assembly of the B. sexangula genome, which was further scaffolded to a pseudomolecule level using the Bruguiera parviflora genome as a reference. The final assembly of the B. sexangula genome contained 260 Mb with an N50 scaffold length of 11,020,310 bp. The assembly comprised 18 pseudomolecules (corresponding to the haploid chromosome number in B. sexangula), covering 204,645,832 bases or 78.6% of the 260-Mb assembly. We predicted a total of 23,978 protein-coding sequences, 17,598 of which were associated with gene ontology (GO) terms. Our gene prediction recovered 96.6% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. The chromosome-level assembly presented in this work provides a valuable genetic resource to help strengthen our understanding of mangroves’ physiological and morphological adaptations to the intertidal zones.

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“…Following the annotation protocol described in Pootakham et al (2021a) , we used evidences from homology-based prediction, RNA-based prediction, and ab initio prediction to identify protein-coding sequences in the unmasked genome assembly using EvidenceModeler (EVM) version 1.1.1 ( Haas et al 2008 ). RNA-based prediction approaches utilized RNA-seq data from C. zippeliana .…”

Section: Methodsmentioning

confidence: 99%

A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome

Pootakham

Sonthirod

Naktang

et al. 2022

G3 Genes|Genomes|Genetics

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Mangroves are of great ecological and economical importance, providing shelters for a wide range of species and nursery habitats for commercially important marine species. Ceriops zippeliana (yellow mangrove) belongs to Rhizophoraceae family and is commonly distributed in the tropical and subtropical coastal communities. In this study, we present a high-quality assembly of the C. zippeliana genome. We constructed an initial draft assembly of 240,139,412 bases with an N50 contig length of 564,761 bases using the 10x Genomics linked-read technology. This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related Ceriops species as a reference. The final assembly contained 243,228,612 bases with an N50 scaffold length of 10,559,178 Mb. The size of the final assembly was close to those estimated using DNA flow cytometry (248 Mb) and the k-mer distribution analysis (246 Mb). We predicted a total of 23,474 gene models and 21,724 protein-coding genes in the C. zippeliana genome, of which 16,002 were assigned gene ontology (GO) terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. The phylogenetic analysis based on single-copy orthologous genes illustrated that C. zippeliana and Ceriops tagal diverged approximately 10.2 million years ago (MYA), and their last common ancestor and Kandelia obovata diverged approximately 29.9 MYA. The high-quality assembly of C. zippeliana presented in this work provides a useful genomic resource for studying mangroves’ unique adaptations to stressful intertidal habitats and for developing sustainable mangrove forest restoration and conservation programs.

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De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements

Cited by 27 publications

References 80 publications

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome

A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome

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