Title:	Chloroplast genome assemblies for four Vanilla species provide targets for the development of molecular markers for species differentiation
Authors:	PAPPAS, M. de C. R. NUNES, T. ALVES, R. de B. das N. ROCHA, F. S. VIEIRA, R. F. BIANCHETTI, L. de B. PAPPAS JÚNIOR, G. J. PESSOA FILHO, M. A. C. de P.
Affiliation:	MARILIA DE CASTRO RODRIGUES PAPPAS, CENARGEN; ROSA DE BELEM DAS NEVES ALVES, CENARGEN; FERNANDO SOUZA ROCHA, CPAC; ROBERTO FONTES VIEIRA, CENARGEN; LUCIANO DE BEM BIANCHETTI, CENARGEN; GEORGIOS J. PAPPAS JÚNIOR, UNIVERSIDADE DE BRASÍLIA; MARCO AURÉLIO CALDAS DE PINHO PESSO, CENARGEN.
Date Issued:	2024
Citation:	In: CONGRESSO NACIONAL DE BOTÂNICA, 74., 2024, Brasília, DF. Botânica Brasileira celebrando a diversidade: livro de resumos. Brasília, DF: Sociedade Botânica do Brasil, 2024
Description:	Vanilla is a valuable spice crop, and continuous initiatives in Brazil have expanded germplasm collections with local species possessing economic potential. These efforts focus on morphological identification, chemical characterization, propagation protocol development, and capacity building. Understanding the genetic diversity and taxonomy of natural populations is crucial for selecting Vanilla species with aromatic potential. Chloroplast genome assemblies for six Vanilla species are publicly available and could provide useful structural and sequence variations for phylogenetic analyses. In this work, we present plastid assemblies for three species (V. phaeantha Rchb. f., V. chamissonis Klotzsch, and V. columbiana Rolfe) for which no genomic information was available, and a new assembly for V. pompona Schiede. Accessions belonging to the Vanilla germplasm collection at Embrapa Recursos Genéticos e Biotecnologia were selected for DNA extraction from previously desiccated and ethanol-treated leaf tissues. Genomic libraries were pooled and paired-end sequenced (2x150bp). Raw reads were trimmed and cleaned of contaminants with BBDuk. Clean reads were input to GetOrganelle v1.7.7.1, with default parameters for plant plastids. For V. phaeantha, word size was set to 102, and a previous incomplete chloroplast assembly obtained with NOVOPlasty was used as seed to generate a complete plastid genome assembly. Assembled genomes were uploaded to the GeSeq web server for semi-automated annotation of CDS, rRNA, organellar tRNAs, and Inverted Repeats (IRs). Graphical maps of chloroplast genome annotations were generated with OGDRAW. Chloroplast genome assembly sizes ranged between 147,372 bp for V. phaeantha and 150,748 for V. calyculata, all of which had a typical structure of one Large Single Copy (LSC) region, two inverted repeats (IRs) and one Short Single Copy (SSC) region. The SSC is exceptionally short in Vanilloideae, and this was observed for the four assemblies, with sizes ranging from 1,962 bp in V. phaeantha to 2,154 bp in V. chamissonis. Manual inspection of annotated regions and a phylogenomic comparison of chloroplast genomes of 11 Vanilla species will be performed, including the new assemblies described in this work and those already available in public databases. Future efforts will also include the identification of insertion/deletion (InDel) regions between species for the design and test of potential PCR-based markers for species differentiation.
NAL Thesaurus:	Plant genetic resources
Keywords:	Phylogenomics
Notes:	Na publicação: Pappas, Marília; Alves, Rosa B. N.: Bianchetti, Luciano B.; Pessoa-Filho, Marco.
Type of Material:	Resumo em anais e proceedings
Access:	openAccess
Appears in Collections:	Resumo em anais de congresso (CENARGEN)