Abstract Detail

Phylogenomics

Meza-Lazaro, Rubi N. [1], Cabrera, Lidia I. [2], Granados Mendoza, Carolina [3], Hágsater, Eric [4], Magallon, Susana [5], Salazar, Gerardo [1].

Chloroplast genomes of two species of Epidendrum (Orchidaceae, Laeliinae): developing resources for evolutionary studies in a mega-diverse genus.

Epidendrum is the most species-rich plant genus in the Neotropics. Its predominantly epiphytic species display a wide array of vegetative architectures and floral sizes, colorations, and fragrances, occurring in nearly every biome from seashore mangroves to high-Andean páramos. Investigating the possible causes underlying such diversity is hampered by the lack of a well-resolved phylogenetic framework. Our efforts to reconstruct Epidendrum phylogenetic relationships using a few Sanger-sequenced loci revealed general patterns, but many clades lacked support or collapsed in consensus trees. Phylogenomic analyses of multiple protein-coding nuclear and plastid loci from a selective genome sampling for a moderate number of taxa offered a promising alternative. However, there is a need for further resolution, whereas resource limitations impose a compromise between taxon-sampling density and data-generation costs. Additionally, the potential of plastome-wide coding vs. non-coding sequences for phylogeny reconstruction remains to be explored. Here we report the first complete chloroplast genomes for two Epidendrum species (E. anisatum and E. marmoratum) obtained through whole genome sequencing (PE150, Illumina HiSeq 2500). We conducted comparative analyses among them and to other plastomes of tribe Epidendreae available in GenBank. The two Epidendrum plastomes are circular molecules with a typical quadripartite structure, attaining a length of 147,580 bp in E. anisatum and 148,807 bp in E. marmoratum. Both have a GC content ~37.5%. Two structural haplotypes were recovered for each plastome, differing in the relative orientation of the short single-copy region. Both Epidendrum plastomes show the same gene order, lack eight nadh genes (ndhJ-ndhK-ndhC, ndhF, and ndhG-ndhI-ndhA-ndhH). Genes ndhD, ndhE and ndhB are pseudogenized, as indicated by multiple indels and internal stop codons. Therefore, there are no functional ndh genes in either of these Epidendrum plastomes, in contrast with those of Masdevallia coccinea (Pleurothallidinae) and Bletia roezlii (Bletiinae), which have a complete set of ndh genes. Gene atpE is duplicated in E. marmoratum but exists as a single copy in E. anisatum. A search for simple-sequence repeats in the non-coding regions of the Epidendrum plastomes found six AT-TA dinucleotides (five repeats), three trinucleotides (four repeats), and one tetranucleotide (three repeats), all shared by both species. The potential of the coding and noncoding sequences to improve tree resolution and support was explored by aligning them with other plastomes and assessing their phylogenetic informativeness under several partitioning schemes. These newly generated plastomic resources will contribute to advancing in phylogenetic resolution and provide insights into plastome evolution in Epidendrum.

1 - Instituto de Biologia, Universidad Nacional Autonoma de Mexico, Botanica, Apartado Postal 70-367, Ciudad Universitaria, Cotoacan, Mexico City, Distrito Federal, 04510, Mexico
2 - Instituto De Biologia, Universidad Nacional Autonoma de Mexico, Botanica, Apartado Postal 70-367, Mexico City, Distrito Federal, 04510, Mexico
3 - Instituto De Biologia, Universidad Nacional Autonoma de Mexico, Apartado Postal 70-367, Héroes de Padierna, Tlalpan, Mexico City, Distrito Federal, 04510, Mexico
4 - Herbario AMO, Instituto Chinoin, Montañas Calizas 490, Lomas de Chapultepec, Mexico City, Distrito Federal, 11000, Mexico
5 - Instituto De Biologia, Universidad Nacional Autonoma de Mexico, Botanica, Apartado Postal 70-367, Héroes de Padierna, Tlalpan, Mexico City, Distrito Federal, 04510, Mexico

Keywords:
coding DNA
Epidendrum
gene loss
Neotropics
non-coding DNA
Orchidaceae
phylogenomics
Plastome.

Presentation Type: Oral Paper
Session: PHYLOII, Phylogenomics II
Location: Virtual/Virtual
Date: Tuesday, July 20th, 2021
Time: 4:15 PM(EDT)
Number: PHYLOII006
Abstract ID:415
Candidate for Awards:None