Research Article Large number of repetitive elements in the draft genome assembly of &lt;i&gt;Dipteryx&lt;/i&gt; &lt;i&gt;alata&lt;/i&gt; (Fabaceae)

Antunes, Adriana Maria; Nunes, Rhewter; Novaes, Evandro; Coelho, Alexandre Siqueira Guedes; Soares, Thannya Nascimento; Telles, Mariana P. C.

doi:10.4238/gmr18463

Cited by 5 publications

(4 citation statements)

References 25 publications

(30 reference statements)

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“…From the results of the present study, the species D. alata was selected for a genomic sequencing project. A draft of the species genome has already been sequenced and annotated (Antunes et al, 2020a) and there is a prospect of generating more sequences to increase the coverage and depth of the D. alata genomic assembly.…”

Section: Resultsmentioning

confidence: 99%

Research Article Genome size and chromosome number of Dipteryx alata (Leguminosae): a model candidate for comparative genomics in Papilionoideae

Antunes¹,

Targueta²,

Castro³

et al. 2020

Genet. Mol. Res.

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Section: Resultsmentioning

confidence: 99%

Research Article Genome size and chromosome number of Dipteryx alata (Leguminosae): a model candidate for comparative genomics in Papilionoideae

Antunes¹,

Targueta²,

Castro³

et al. 2020

Genet. Mol. Res.

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“…In this study, the data generated by Illumina platform allowed us to assemble part of the genome of P. emarginatus and discover thousands of microsatellites regions. Draft assemblies with low coverage were used to detect microsatellite regions and design large-scale primers for other species, such as Dipteryx alata Vogel and Passiflora edulis Sims [ 9 , 27 , 28 ].…”

Section: Discussionmentioning

confidence: 99%

A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data

Antunes

Stival

Targueta

et al. 2022

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Background: Also known as simple sequence repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusions: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.

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“…Fabaceae is considering a large and economically vital family of flowering plants which is usually known as the legume family [1][2][3][4][5]. The Fabaceae family, which has over 490 medicinal plant species 730 genera flowering plants and more than 19,400 species [5][6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Endorsement and phylogenetic analysis of some Fabaceae plants based on DNA barcoding

et al. 2022

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Background DNA barcoding have been considered as a tool to facilitate species identification based on its simplicity and high-level accuracy in compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene (MatK gene) of the chloroplast is very vital in the plant system which is involved in the group II intron splicing. The main objective of this study is to determine the relative utility of the “MatK” chloroplast gene for barcoding in 15 legume as a tool to facilitate species identification based on their simplicity and high-level accuracy linked to morphological identification of taxa. Methods and Results MatK gene sequences were submitted to GenBank and the accession numbers were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server, Clustal Omega server and Bioedit program. Maximum likelihood and neighbor-joining algorithms were employed for constructing phylogeny. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna, Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade. Conclusion Moreover, their sequences could be successfully utilized in single nucleotide polymorphism or as part of the sequence as DNA fragment analysis utilizing polymerase chain reaction in plant systematic. Therefore, MatK gene is considered promising a candidate for DNA barcoding in the plant family Fabaceae and provides a clear relationship between the families.

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Research Article Large number of repetitive elements in the draft genome assembly of <i>Dipteryx</i> <i>alata</i> (Fabaceae)

Cited by 5 publications

References 25 publications

Research Article Genome size and chromosome number of <i>Dipteryx</i> <i>alata</i> (Leguminosae): a model candidate for comparative genomics in Papilionoideae

Research Article Genome size and chromosome number of <i>Dipteryx</i> <i>alata</i> (Leguminosae): a model candidate for comparative genomics in Papilionoideae

A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data

Endorsement and phylogenetic analysis of some Fabaceae plants based on DNA barcoding

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