Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Abstract

Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

“…Emerging long-read sequencing technologies, such as Pacific Bioscience (PacBio) and Oxford Nanopore Technology (ONT), have led to substantial advances in resolution of chromosomal structures including highly repetitive sequences such as centromeres. Using these technologies, centromeres that were difficult to resolve using short-read sequencing, were defined in various organisms, from fungi (12, 19, 20) to insects (21), plants (22) and humans (23).…”

Selection pressure causes differentiation of the SPL gene family in the Juglandaceae

“…The expression patterns of Clade 1.3 did not differ much from those of the other two branches, so the Clade 1.3 genes may redundantly regulate plant growth and development along with the genes in the other branches in Clade 1. Lan et al (2017) described that an individualized genomic architecture might play an important role in adaptation to specific environments when plants are under purifying selection. From the above observation, we speculate that when an environment changes considerably, the SPL genes of Clades 1.1 and 1.2 will continue to play their original roles, while those of Clade 1.3 can develop further.…”

Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics

“…Four were available: Cephalotup follicularip (Fukushima, Fang, et al, 2017), Dropera capenpip (Butts, Bierma, & Martin, 2016), Genlipea aurea (Leushkin et al, 2013), and Utricularia gibba (Lan et al, 2017). The carnivorous taxa sampled represent three independent origins of plant carnivory (Genlipea and Utricularia likely sharing a single origin) in three plant orders (Caryophyllales, Oxalidales, and Lamiales).…”