Assembly of the durian chloroplast genome using long PacBio reads

Shearman, Jeremy R.; Sonthirod, Chutima; Naktang, Chaiwat; Sangsrakru, Duangjai; Yoocha, Thippawan; Chatbanyong, Ratchanee; Vorakuldumrongchai, Siriporn; Chusri, O.; Tangphatsornruang, Sithichoke; Pootakham, Wirulda

doi:10.1038/s41598-020-73549-4

Cited by 18 publications

(15 citation statements)

References 27 publications

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“…For instance, nine genes were transferred from the SSC to the IR region in Plantago ovata resulting in an extremely long IR (37.4 kb) 25 as compared to IR found in the other plastomes which normally range between 25 kb and 30 kb 40 . In contrast, the loss of IR had been reported in the plastomes of 25 durian varieties recently 37 .…”

Section: Discussionmentioning

confidence: 87%

“…In this study, a complete mangosteen plastome of Mesta variety (156,580 bp) was successfully obtained from PacBio long reads. Here, the use of long reads for the assembly of the plastid genomes was ideal to obtain longer contigs and to resolve repetitive regions 26,36,37 . In addition, Illumina sequencing data were used to correct the random errors within PacBio reads 38 .…”

Section: Discussionmentioning

confidence: 99%

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Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Wee

Muhammad

Subbiah

et al. 2022

Preprint

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The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety which was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.

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Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Wee

Muhammad

Subbiah

et al. 2022

Preprint

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“…This effect is more pronounced in tetraploid genomes, since they have more alternative haplotype versions of the same region. Long-read sequencing technologies such as PacBio ( Shearman et al 2020 ; Vollger et al 2020 ) and Nanopore ( Kuderna et al 2019 ; Low et al 2019 ; Kinkar et al 2021 ) aim to overcome the problem of heterozygosity, allowing more space for overlaps during assembly ( Jiao and Schneeberger 2017 ). Further sequencing technologies such as proximity ligation and optical mapping help resolving areas that are difficult to assemble ( Field et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety

Freire

Weisweiler

Guerreiro

et al. 2021

G3 Genes|Genomes|Genetics

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Potato (Solanum tuberosum L.) is one of the most important crops with a world-wide production of 370 million metric tons. The objectives of this study were (i) to create a high quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (ii) to evaluate the new assembly’s usefulness for various genomic methods and (iii) to assess the performance of phasing in diploid and tetraploid clones, using linked read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity-ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.

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“…A total of 18 genes had introns, and three genes ( ycf3 , clpP, and rps12 ) contained two introns. Despite typically highly conserved, gene relocation and structural variation in IR and single-copy regions are very common ( de Santana Lopes et al, 2018 ; Shearman et al, 2020 ; Guo et al, 2021 ). The cp genome structures of 10 representative Acer species are shown in Supplementary Figure S1 .…”

Section: Resultsmentioning

confidence: 99%

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

Gao

Liao

et al. 2022

Front. Genet.

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Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124–156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103–158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76–103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.

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Assembly of the durian chloroplast genome using long PacBio reads

Cited by 18 publications

References 27 publications

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

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