Project description:As a serious forest pest on coniferous trees, Dendrolimus kikuchii has caused widespread concern in China. Here, its complete mitochondrial genome (mitogenome) has been sequenced with 15,382 bp in length. The mitogenome has a base composition of A (40.87%), T (37.83%), C (13.43%), and G (7.87%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and an A + T-rich region. The phylogenetic relationships among the lasiocampid species were (Trabala vishnou+ ((Apatelopteryx phenax+ Euthrix laeta) + (Dendrolimus kikuchii+ (D. spectabilis+ (D. tabulaeformis + D. punctatus))))), which were supported by a posterior probability of 1.00 and a high bootstrap value of 100%.

| S-EPMC7799951 | biostudies-literature

High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii.

Project description:Plant diseases caused by the Cercospora genus of ascomycete fungi are a major concern for commercial agricultural practices. Several Cercospora species can affect soybeans, such as Cercospora kikuchii which causes soybean leaf blight. Speciation in Cercospora on soybean has not been adequately studied. Some cryptic groups of Cercospora also cause diseases on soybean. Moreover, it has been known C. kikuchii population genetic structure is different between countries. Consequently, further genomic information could help to elucidate the covert differentiation of Cercospora diseases in soybean. Here, we report for the first time, a chromosome-level genome assembly for C. kikuchii. The genome assembly of 9 contigs was 34.44 Mb and the N50 was 4.19 Mb. Based on ab initio gene prediction, several candidates for pathogenicity-related genes, including 242 genes for putative effectors, 55 secondary metabolite gene clusters, and 399 carbohydrate-active enzyme genes were identified. The genome sequence and the features described in this study provide a solid foundation for comparative and evolutionary genomic analysis for Cercospora species that cause soybean diseases worldwide.

| S-EPMC8496228 | biostudies-literature

Mitochondrial DNA markers reveal high genetic diversity and strong genetic differentiation in populations of Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae).

Project description:Dendrolimus kikuchii Matsumura, 1927 is a serious forest pest causing great damage to coniferous trees in China. Despite its economic importance, the population genetics of this pest are poorly known. We used three mitochondrial genes (COI, COII and Cytb) to investigate the genetic diversity and genetic differentiation of 15 populations collected from the main distribution regions of D. kikuchii in China. Populations show high haplotype and nucleotide diversity. Haplotype network and phylogenetic analysis divides the populations into three major clades, the central and southeastern China (CC+SEC) clade, the eastern China (EC) clade, and the southwestern China (SWC) clade. Populations collected from adjacent localities share the same clade, which is consistent with the strong relationship of isolation by distance (r = 0.74824, P = 0.00001). AMOVA analysis indicated that the major portion of this molecular genetic variation is found among the three groups of CC+SEC, EC and SWC (61.26%). Of 105 pairwise FST comparisons, 93 show high genetic differentiation. Populations of Puer (PE), Yangshuo (YS) and Leishan (LS) are separated from other populations by a larger genetic distance. Distributions of pairwise differences obtained with single and combined gene data from the overall populations are multimodal, suggesting these populations had no prior population expansion in southern China. The nonsignificant neutral test on the basis of Tajima' D and Fu's Fs, and the lack of a star-shaped haplotype network together with the multiple haplotypes support this hypothesis. Pleistocene climatic fluctuations, combined with the host specificity to Pinus species, made these regions of south China into a refuge for D. kikuchii. The high level of population genetic structuring is related to their weak flight capacity, their variations of life history and the geographic distance among populations.

| S-EPMC5491029 | biostudies-literature

Complete mitochondrial genome of Simao pine caterpillar moth, <i>Dendrolimus kikuchii</i> (Lepidoptera: Lasiocampidae) and the related phylogenetic analysis.

Project description:Dendrolimus kikuchii, the Simao pine caterpillar moth is an economically important forest pest causing great damage to coniferous trees in south China. The whole mitogenome for the moth was sequenced using next-generation sequencing technology. The moth has a total length of 15,422 bp in mitogenome size. The nucleotide composition is biased toward adenine and thymine, accounting for 79.2%: A = 40.7%, T = 38.5%, G = 8.1%, and C = 12.7%. The phylogeny showed that D. kikuchii was closely grouped with D. punctatus, D. tabulaeformis, Euthrix laeta, and Trabala vishnou guttata to form the monophyletic clad for the Lasiocampidae family of Bombycoidea superfamily with strong nodal support.

| S-EPMC7800353 | biostudies-literature

Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor Tbx6b in the ascidian early gastrula embryo.

2010-03-09 | GSE17694 | GEO

SoxC ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor SoxC in the ascidian early gastrula embryo.

2010-03-09 | GSE17692 | GEO