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High-quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola).

ABSTRACT: The collembolan Folsomia candida Willem, 1902, is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal "standard" because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we obtained two high-quality chromosome-level genomes of F. candida, for a parthenogenetic strain (named FCDK, 219.08 Mb, 25,139 protein-coding genes) and a sexual strain (named FCSH, 153.09 Mb, 21,609 protein-coding genes), reannotated the genome of the parthenogenetic strain reported by Faddeeva-Vakhrusheva et al. in 2017 (named FCBL, 221.7 Mb, 25,980 protein-coding genes) and conducted comparative genomic analyses of the three strains. High genome similarities between FCDK and FCBL based on synteny, genome architecture, mitochondrial and nuclear gene sequences suggest that they are conspecific. The seven chromosomes of FCDK are each 25%-54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to the broader environmental adaptation of parthenogenetic strains. In addition, FCDK has fewer strain-specific microRNAs than FCSH, and their mitochondrial and nuclear genes have diverged greatly. In conclusion, FCDK/FCBL and FCSH have accumulated independent genetic changes and evolved into distinct species after 10 million years ago. Our work provides important genomic resources for studying the mechanisms of rapidly cryptic speciation and soil arthropod adaptation to soil ecosystems.

SUBMITTER: Luan YX

PROVIDER: S-EPMC10087712 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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High-quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola).

Luan Yun-Xia YX Cui Yingying Y Chen Wan-Jun WJ Jin Jian-Feng JF Liu Ai-Min AM Huang Cheng-Wang CW Potapov Mikhail M Bu Yun Y Zhan Shuai S Zhang Feng F Li Sheng S

Molecular ecology resources 20220905 1

The collembolan Folsomia candida Willem, 1902, is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal "standard" because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we obtained two high-quality chromosome-level genomes of F. candida, for a parthenogenetic strain (named FCDK, 219.08 Mb, 25,139 ...[more]

PMID: 35962787

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Project description:Abstract Litter quality has long been associated with demographic parameters of Collembola populations. However, little is known about the capacity of Collembola to perceive and seek better litter quality. To address this gap, three complementary laboratory experiments were carried out with the Collembola Folsomia candida. First, populations were fed on three different types of leaf litters (Quercus pubescens, Acer opalus and Prunus avium) and a control (agar‐agar‐brewer's yeast mixture) for 6 weeks to assess their impacts on demography (reproduction rate and population size). Second, the body length of individuals differentially fed with the same four types of resources was measured to assess a functional trait that can potentially affect movement parameters such as prospected area or foraging speed. Third, F. candida single individuals were exposed to the same litter quality gradient and placed at an increasing distance from the litter (from 1 to 5 cm). For 10 min, their foraging behaviour was recorded which included prospected area, foraging speed, perception distance and success in reaching the litter (foraging success). As expected, low‐quality litter (i.e. Q. pubescens) contributed to low population growth compared to the control treatment and the high‐quality litters (P. avium and A. opalus). In the third experiment, the probability of finding the resource was negatively correlated to the distance, but was unrelated to the litter quality and the Collembola body length. When resource was perceived, F. candida was able to switch from non‐directional to directional movements, with a large variability in the perception distance from a few millimetres to several centimetres. Taken together, our results indicate that litter quality plays a relevant role in Collembola demographic parameters once the population settles on litter patch, but not on foraging behaviour to select high‐quality resources. Embark on a captivating exploration of Folsomia candida, as we unravel the effects of litter quality on its foraging behavior and demographic dynamics. Discover how resource quality shapes carrying capacity and gain insights into unexpected foraging strategies.

Project description:BACKGROUND: The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, which have major socio-economic impacts. Pathogenicity is an ancestral trait in R. solanacearum and strains with high genetic variation can be subdivided into four phylotypes, correlating to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB), Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome sequences strains representative of this phylogenetic diversity can help determine which traits allow this bacterium to be such a pathogen of so many different plant species and how the bacteria survive in many different habitats. RESULTS: The genomes of three tomato bacterial wilt pathogens, CFBP2957 (phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were sequenced and manually annotated. These genomes were compared with those of three previously sequenced R. solanacearum strains: GMI1000 (tomato, phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The major genomic features (size, G+C content, number of genes) were conserved across all of the six sequenced strains. Despite relatively high genetic distances (calculated from average nucleotide identity) and many genomic rearrangements, more than 60% of the genes of the megaplasmid and 70% of those on the chromosome are syntenic. The three new genomic sequences revealed the presence of several previously unknown traits, probably acquired by horizontal transfers, within the genomes of R. solanacearum, including a type IV secretion system, a rhi-type anti-mitotic toxin and two small plasmids. Genes involved in virulence appear to be evolving at a faster rate than the genome as a whole. CONCLUSIONS: Comparative analysis of genome sequences and gene content confirmed the differentiation of R. solanacearum species complex strains into four phylotypes. Genetic distances between strains, in conjunction with CGH analysis of a larger set of strains, revealed differences great enough to consider reclassification of the R. solanacearum species complex into three species. The data are still too fragmentary to link genomic classification and phenotypes, but these new genome sequences identify a pan-genome more representative of the diversity in the R. solanancearum species complex.

Dataset Information

High-quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola).

Publications

High-quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola).

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