The Apostasia genome and the evolution of orchids

Abstract

Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1-3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel thirdgeneration genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.

Ancestral duplicatedDL/CRCorthologs display function on orchid reproductive organ innovation

“…Zhang et al (2017) indicated the possibility of an ancient orchid-specific whole-genome duplication (WGD) event shared by all extant orchids, which might be correlated with orchid diversification. Interestingly, it has been reported that DL/CRC represents a single orthologous lineage, without ancient duplications (Lee et al , 2005).…”

“…The conserved YAB domain based on the hidden Markov model (HMM) (PF04690) was obtained from the Pfam protein family database (http://pfam.sanger.ac.uk). To identify the YABBY transcription factor coding genes of orchids, the HMM profile of the YABBY domain was used as a query for an HMMER search (http://hmmer.janelia.org/) of the P. equestris , Dendrobium catenatum , and Apostasia shenzenica genome sequences (E-value=0.00001) (Cai et al , 2015; Zhang et al , 2016; Zhang et al , 2017).…”

Genome structure and evolution ofAntirrhnum majusL

“…Although Antirrhinum did not experience a whole genome triplication, the duplicated region containing TCP genes on chromosomes 6 and 8 are closely associated with zygomorphic flower type, showing its unique evolutionary manner because no similar mechanism had been found in closely related species. For examples, one separated whole genome duplication led to partial zygomorphic type species of Glycine; and a MADS box family gene change resulting in symmetrical flowers in Orchidaceae 26,27 . In general, the ancient species are mostly radial symmetry and the newly derived species with symmetrical flowers.…”

De novogenome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies

“…The, Linked-reads technology (10x Genomics), has emerged as an alternative approach to obtain long-range sequence information and even construct haplotype specific assemblies while leveraging the high throughput, low cost, and accuracy of short-read sequencing. Recent de novo genome assembly projects have opted to combine different technologies [43][44][45] highlighting the benefit of hybrid genome assembly. Particularly important is the combination of highly accurate short-read SGS technologies with long-read TGS technologies.…”