Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding

Abstract

Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle in vitro make E. pusilla a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of E. pusilla was sequenced accurately, efficiently and economically. The cp genome of E. pusilla shares 89 and 84% similarity with Oncidium Gower Ramsey and Phalanopsis aphrodite, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the rps15-trnN region of the Cymbidieae tribe. Because commercial Oncidium varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of E. pusilla, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that trnF-ndhJ and trnH-psbA were suitable for phylogenetic analysis. E. pusilla proved to be phylogenetically closer to Rodriguezia and Tolumnia than Oncidium, despite its similar floral appearance to Oncidium. These results indicate the hybrid compatibility of E. pusilla, its cp genome providing important information for Oncidium breeding.

Figure 1. Gene map of Erycina pusilla chloroplast genome.

Genes on the outside of the map are transcribed clockwise whereas genes on the inside of the map are transcribed counterclockwise. Colors indicate genes with different functional groups.

Figure 2. Comparison of chloroplast genomes of E. pusilla, Onc. Gower Ramsey, and P. Aphrodite.

Deletions or insertions longer than 70 bp in P. aphrodite or Onc. Gower Ramsey in comparison with E. pusilla are labeled as white triangles or black triangles individually. Highly diverse sequence regions larger than 500 bp are labeled with black blocks. Numbers indicate the longest length of comparative deletions, insertions, or diverse sequence retions of three species orchids.

Figure 3. Structure of ndh genes in 3 orchid cp genomes.

Numbers indicate the position in the chloroplast genome. The angled dashed lines indicate the gaps. Different colors indicate different ndh genes, a color key is shown at the bottom of each part of the Figure. Accession number of O. sative Japonica is NC_001320.

Figure 4. Variations in 5 regions in 19 Epidendroideae species.

Numbers indicate the positions of the chloroplast genome. The angled dashed lines indicate deletions. The green triangle indicates an insertion. The yellow areas indicate diverse sequences. ¹including Calanthe discolor and Calanthe sylvatica; ²including Geodorum densiflorum; ³including Cymbidium aloifolium and Geodorum densiflorum.

Figure 5. Phylogenetic analysis of 36 Oncidiinae species.

These trees are based on the nucleotide sequences of A. trnF-ndhJ, B. trnF-ndhJ and trnH-psbA cpDNA regions. The numbers indicate bootstrap probability values. The names of genera are abbreviated as follows: Bllra., Beallara; Comp., Comparettia; Dgmra., Degarmoara; Incdm., Ionocidium; Mac., Macradenia; Mtssa., Miltassia; Odm., Odontoglossum; Odcdm., Odontocidium; Onc., Oncidium; P., Phalaenopsis; , Rod., Rodriguezia; and Tol., Tolumnia.