The Streptochaeta Genome and the Evolution of the Grasses

Abstract

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.

Genetic control of branching patterns in grass inflorescences

“…euAP2- like genes have two AP2 domains ( Kim et al, 2006 ), rather than the single domain found in FZP . In addition, nearly all genes in this group also have miR172 binding sites ( Seetharam et al, 2021 ) and miR172 expression opposes expression of AP2- like genes ( Figure 5A ). The AP2- like -miR172 interaction has been investigated for its role in specifying the number of florets per spikelet (e.g.…”

“…In wheat, the IDS ortholog is the domestication gene Q ( Seetharam et al, 2021 ), which is also regulated by miR172 ( Debernardi et al, 2017 ). The transition to forming glumes is particularly obvious in wheat because the glumes have prominent keels, shorter awns, and more sclerenchyma than lemmas.…”

A lineage-specific Exo70 is required for receptor kinase–mediated immunity in barley

“…Our initial analysis encompassed genomes from eight Poaceae species. To ascertain the origin of the Exo70FX clade, we identified Exo70 clade members in the recently sequenced genomes of Streptochaeta angustifolia ( 46 ) and Pharus latifolius ( 47 ), which represent critical species at the boundary of the Poaceae family. In addition, we included Ananas comosus (pineapple; Poales, Bromeliaceae) ( 48 ) and Musa acuminata (banana; Zingiberales, Musaceae) ( 49 ).…”

Tandem duplications, eupolyploidy and secondary diploidization – genetic mechanisms of plant speciation and progressive evolution

“…На разных этапах существования полиплоида потеря генов происходит с разной интенсивностью -как правило, на стадии неополиплоида идут многочисленные перестройки генома (Xiong et al, 2011;Buggs et al, 2012) В процессе фракционирования нео-и мезополиплоидных геномов разных видов, по комплектам сохранившихся в дуплицированном состоянии и оставшихся в единичных копиях генов геномы растений всех филогенетических ветвей оказываются различны, что может рассматриваться как причина морфологических различий между таксонами. Так, сильно измененные в сравнении с другими Poaceae колоски архаичной ветви Streptochaeta, по-видимому, появились после того, как геном Streptochaeta потерял одну из двух копий, влияющих на морфологию колоска генов fruitfull (ful) и leafy hull sterile1 (lhs1), дублированных у общего предка Poaceae и в дублированном состоянии сохранившихся у остальных злаков (Seetharam et al, 2021). Напротив, гены, кодирующие факторы транскрипции и влияющие на морфологию колоска frizzy panicle (fzp) и branched silkless1 (bd1) в геномах «продвинутых» злаков дуплицированы, а у имеющего особые по строению колоски архаичного Pharus latifolius сохранились только в одной копии (Ma et al, 2021).…”

“…После дупликации исходный ген и его новообразованные копии могут сосуществовать в геноме десятки и сотни млн лет (Panchy et al, 104 Родионов А. В. Механизмы видообразования и прогрессивной эволюции 2016; Ma et al, 2021;Seetharam et al, 2021;Yuan et al, 2021). Судьба у новообразованных дочерних копий гена может быть разная.…”