We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.

Subterranean clover (Trifolium subterraneum L.) is the most widely sown annual pasture legume species in southern Australia, valued in the livestock and grains industries as a source of high-quality forage and for its ability to fix atmospheric nitrogen. From its initial accidental introduction into Australia in the 19th Century and subsequent commercialisation in the early 1900s, 45 cultivars have been registered in Australia. These consist of 32 cultivars of ssp. subterraneum, eight of ssp. yanninicum, and five of ssp. brachycalycinum and range in flowering time from 77 to 163 days from sowing, enabling the species to be grown in a diversity of rainfall environments, soil types, and farming systems. Eleven of these cultivars are introductions from the Mediterranean region, 15 are naturalised strains collected in Australia, 18 are the products of crossbreeding, and one is derived from mutagenesis. Cultivars developed in Italy have been commercialised for the local market, whereas other cultivars developed in Spain, Portugal, and France have not had commercial seed production. Important traits exploited include: (i) selection for low levels of the oestrogenic isoflavone formononetin, which causes reduced ewe fertility; (ii) increased levels of dormancy imposed by seed-coat impermeability (hard seeds) for cultivars aimed at crop rotations or unreliable rainfall environments; (iii) strong burr-burial ability to maximise seed production; (iv) resistance to important disease pathogens for cultivars aimed at medium- and high-rainfall environments, particularly to Kabatiella caulivora and root rot pathogens; (v) resistance to pests, particularly redlegged earth mites; and (vi) selection for unique leaf markings and other morphological traits (where possible) to aid cultivar identification. Cultivar development has been aided by a large genetic resource of ~10 000 accessions, assembled from its centre of origin in the Mediterranean Basin, West Asia, and the Atlantic coast of Western Europe, in addition to naturalised strains collected in Australia. The development of a core collection of 97 accessions, representing almost 80% of the genetic diversity of the species, and a genetic map, provides a platform for development of future cultivars with new traits to benefit the livestock and grains industries. New traits being examined include increased phosphorous-use efficiency and reduced methane emissions from grazing ruminant livestock. Economic analyses indicate that future trait development should focus on traits contributing to increased persistence and autumn–winter productivity, while other potential traits include increased nutritive value (particularly of senesced material), increased N2 fixation ability, and tolerance to cheap herbicides. Beneficial compounds for animal and human health may also be present within the species for exploitation.

Microchromosomes, once considered unimportant shreds of the chicken genome, are gene-rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole-genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds, and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly, de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early-branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently, multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus, microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles and birds, that are atypical.

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Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover (T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover (T. pratense) and white clover (T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.

Diverse signaling pathways are activated by perturbation of mitochondrial function under different growth conditions. Mitochondria have emerged as an important organelle for sensing and coping with stress in addition to being the sites of important metabolic pathways. Here, responses to moderate light and drought stress were examined in different Arabidopsis (Arabidopsis thaliana) mutant plants lacking a functional alternative oxidase (alternative oxidase1a [aox1a]), those with reduced cytochrome electron transport chain capacity (T3/T7 bacteriophage-type RNA polymerase, mitochondrial, and plastidial [rpoTmp]), and double mutants impaired in both pathways (aox1a:rpoTmp). Under conditions considered optimal for growth, transcriptomes of aox1a and rpoTmp were distinct. Under adverse growth conditions, however, transcriptome changes in aox1a and rpoTmp displayed a highly significant overlap and were indicative of a common mitochondrial stress response and downregulation of photosynthesis. This suggests that the role of mitochondria to support photosynthesis is provided through either the alternative pathway or the cytochrome pathway, and when either pathway is inhibited, such as under environmental stress, a common, dramatic, and succinct mitochondrial signal is activated to alter energy metabolism in both organelles. aox1a:rpoTmp double mutants grown under optimal conditions showed dramatic reductions in biomass production compared with aox1a and rpoTmp and a transcriptome that was distinct from aox1a or rpoTmp. Transcript data indicating activation of mitochondrial biogenesis in aox1a:rpoTmp were supported by a proteomic analysis of over 200 proteins. Under optimal conditions, aox1a: rpoTmp plants seemed to switch on many of the typical mitochondrial stress regulators. Under adverse conditions, aox1a:rpoTmp turned off these responses and displayed a biotic stress response. Taken together, these results highlight the diverse signaling pathways activated by the perturbation of mitochondrial function under different growth conditions.

SummarySubterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1.1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano‐based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super‐scaffolds (43% of genome). Sequences longer than >1 Mb increased from 40 to 189 Mb giving 1.4‐fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re‐annotated using transcriptome atlas data to contain 31 272 protein‐coding genes capturing >96% of the gene content. Functional characterization and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24 893 Trifolium‐specific and 6325 subterranean‐clover‐specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro‐morphological traits, were fine‐mapped on the high‐density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker‐assisted breeding, comparative mapping and identification of tissue‐specific gene promoters for biotechnological improvement of forage legumes.

Peas (Pisum sativum L.) are exposed to waterlogging at germination when grown as relay in rice‐based cropping. Ninety‐one germplasm accessions were evaluated in relay (sown in waterlogged soil), and subsequently 10 diverse genotypes compared under relay and sole cropping (conventional tillage sowing) over two seasons in Bangladesh. Contrasting genotypes, BM‐3, NL‐2 and Kaspa, were further evaluated in three waterlogging treatments (drained control, 4 and 8 days waterlogging) in the glasshouse. Conspicuous variation in waterlogging tolerance at germination was observed in the field and confirmed under controlled conditions. In relay sowing in 2011, emergence of a few genotypes was affected by waterlogging. In 2012, emergence in relay was severely affected (12 plants/m2) compared to sole sowing (37 plants/m2). Among genotypes BM‐3 had 6 plants/m2 emerge, which all subsequently died, in contrast to NL‐2 in which emergence was 13 plants/m2 with all plants surviving. In the glasshouse, there was 14% emergence in BM‐3, 40% in NL‐2 and 55% in Kaspa after 8 days of waterlogging. Such marked differences in waterlogging tolerance at germination in the model pea are the first reported and illustrate prospects for selection to improve adaptation to relay sowing in South Asia.