Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown.Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched inC. rubellacompared with its outcrossing sister speciesCapsella grandiflora, and (ii) 4.2% of polymorphic TEs inC. rubellaare associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions atFLOWERING LOCUS C (FLC)in natural populations ofC. rubellacould explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR ofFLCaffects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.

Lateral organ boundaries (LOB) domain (LBD) genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At present, though there have been a number of genome-wide analyses on LBD gene families and functional studies on individual LBD proteins, the diverse functions of LBD family members still confuse researchers and an effective strategy is required to summarize their functional diversity. To further integrate and improve our understanding of the phylogenetic classification, functional characteristics and regulatory mechanisms of LBD proteins, we review and discuss the functional characteristics of LBD proteins according to their classifications under a phylogenetic framework. It is proved that this strategy is effective in the anatomy of diverse functions of LBD family members. Additionally, by phylogenetic analysis, one monocot-specific and one eudicot-specific subclade of LBD proteins were found and their biological significance in monocot and eudicot development were also discussed separately. The review will help us better understand the functional diversity of LBD proteins and facilitate further studies on this plant-specific transcription factor family.

Background: Small heat shock proteins (sHSPs) are products of heat shock response and of other stress responses, and ubiquitous in all three domains of life, archaea, bacteria, and eukarya. They mainly function as molecular chaperones to protect proteins from being denatured in extreme conditions. Study on insect sHSPs could provide some insights into evolution of insects that have adapted to diverse niches in the world. Results: Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate sHSP genes in the silkworm, Bombyx mori. Based on known silkworm sHSP sequences, we identified 16 silkworm sHSP genes. Most of them are distributed on two silkworm chromosomes 5 and 27, respectively. 15 of 16 silkworm sHSPs have expression evidence. The comparative analysis of insect sHSPs from B. mori, Drosophila melanogaster, Apis mellifera, Tribolium castaneum, and Anopheles gambiae revealed that there is only one orthologous cluster whereas remaining clusters are species-specific on the phylogenetic tree. This suggested that most of sHSPs might have diverged in function across insects investigated. In addition, the data presented in this study also revealed that sHSPs in the insect orthologous cluster are highly conserved in both sequence and expression pattern. In sum, insect sHSPs show a completely different evolutionary pattern from that found in vertebrate sHSPs. Conclusion: B. mori has the largest number of insect sHSP genes characterized to date, including 16 genes. The inference that most species-specific sHSPs might have diverged in function across insects investigated will help us understand the adaptability of these insects to diverse environments.

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping. A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.