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Genome Rearrangement Shapes Prochlorococcus Ecological Adaptation.

ABSTRACT: Prochlorococcus is the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles. Prochlorococcus can be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted clade I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructed Prochlorococcus evolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role in Prochlorococcus evolution. We also found that the Prochlorococcus clades with streamlined genomes maintained relatively high synteny throughout most of their genomes, and several regions served as rearrangement hotspots. Backbone analysis showed that different clades shared a conserved backbone but also had clade-specific regions, and the genes in these regions were associated with ecological adaptations.IMPORTANCE Prochlorococcus, the most abundant and smallest known free-living photosynthetic microorganism, plays a key role in marine ecosystems and biogeochemical cycles. Prochlorococcus genome evolution is a fundamental issue related to how Prochlorococcus clades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted the Prochlorococcus genome evolution from the perspective of genome structure and associated the genome rearrangement with the Prochlorococcus clade differentiation and subsequent ecological adaptation.

SUBMITTER: Yan W

PROVIDER: S-EPMC6102989 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:As an elite rice variety cultivated in the third accumulative temperature belt in Heilongjiang province, China, Kongyu131 has many excellent traits, such as high quality, high stability, early maturation and cold resistance. However, as with other crop varieties, Kongyu131 has regional restrictions, exhibiting decreased yields when grown at low latitudes. To address these problems, two populations were constructed from cross between japonica and indica varieties. QTL analyses were performed with these two populations to detect regional adaptation related quantitative trait locus. Results in a BC1F6 backcross inbred line population with 168 lines derived from cross between Kongyu131 and GKMP showed a large pleiotropic QTL near 9 Mb on chromosome 7, which significantly delayed the HD of Kongyu131 and increased the plant height (PH), length of main panicle (LMP), number of primary branches (NPB) and grain number of main panicles (GNP). We also found a similar QTL in the population BC3F2 derived from Kongyu131 and GKLPL. Based on the QTL, we developed a gene module named mRA7 with 5 single-nucleotide polymorphism (SNP) markers around the QTL. Through a foreground and background selection based on 197 SNP markers evenly distributed over the 12 chromosomes, we obtained a new plant (a single point substitution line, SPSL) with a new Kongyu131 genome, carrying only a small chromosomal fragment less than 800 kb from GKLPL. The background recovery ratio of the SPSL was 99.8%. Compared with Kongyu131, the SPSL exhibited a significant HD delay of approximately 31 days and increased PH, LMP and GNP values when planted in Heilongjiang province. When cultivated in Guangdong province, HD of SPSL showed only 16 days delay, and less increase in PH, LMP and GNP than in Heilongjiang province. Phenotypic evaluation showed that the SPSL could be moved to south by more than 3 latitude units and cultivated in low-latitude regions. This study exemplifies the feasibility of expanding the regions of cultivation of elite rice varieties via similar methods.

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Genome Rearrangement Shapes Prochlorococcus Ecological Adaptation.

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