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Abstract Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time. 

In this work, we sequenced and annotated the genome of Streptochaeta angustifolia , one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions. 

Abstract Bamboos are a diverse and ecologically important group of plants that have the potential to modulate the structure, composition, and function of forests. With the aim of increasing the visibility and representation of bamboo in forest surveys, and to standardize techniques across ecosystems, we present a protocol for bamboo monitoring in permanent research plots. A bamboo protocol is necessary because measurements and sampling schemes that are well‐suited to trees are inadequate for monitoring most bamboo species and populations. Our protocol suggests counting all bamboo culms (stems) in the study plot and determining bamboo dimensions based on two different approaches: (a) measuring a random subset of 60 culms and calculating the average dimensions or (b) measuring all culms. With data from 1‐ha plots in the Peruvian Andes, we show that both approaches provide very similar estimates of bamboo basal area. We suggest including all mature culms rooted inside change the to each plot from all woody bamboo species with maximum diameters ≥1 cm. We also present recommendations on how to collect vouchers of bamboo species for identification. Data collected according to our proposed protocols will increase our understanding of regional and global patterns in bamboo diversity and the role of bamboo in forest dynamics. Abstract in Spanish is available with online material.