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Characterization of the mitochondrial genome of the plain flowerpecker, Dicaeum concolor (Dicaeidae) from Yunnan Province, China.

ABSTRACT: The plain flowerpecker, Dicaeum concolor, is a tiny bird classified in the flowerpecker family Dicaeidae, and is an important pollinator and disperser of mistletoes in forests. This species is distributed across South and Southeast Asia. For further phylogeographic studies of D. concolor, the complete mitochondrial genome was sequenced here. The genome (GenBank accession no. MW429430) is 16,796 bp in length and comprises 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs. The GC content of the genome sequence is 45.46%, with an overall base composition of 30.76% A, 30.92% C, 14.53% G, and 23.79% T. A maximum-likelihood analysis placed D. concolor as sister relationship to D. eximium. The mitochondrial genome of the plain flowerpecker will be useful for studies of molecular evolution in flowerpeckers.

SUBMITTER: Gao Y

PROVIDER: S-EPMC8344764 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Yunnan Province, China is thought to be the original source of biovar Orientalis of Yersinia pestis, the causative agent of the third plague pandemic that has spread globally since the end of the 19th century. Although encompassing a large area of natural plague foci, Y. pestis strains have rarely been found in live rodents during surveillance in Yunnan, and most isolates are from rodent corpses and their fleas. In 2017, 10 Y. pestis strains were isolated from seven live rodents and three fleas in Heqing County (HQ) of Yunnan. These strains were supposed to have low virulence to local rodents Eothenomys miletus and Apodemus chevrieri because the rodents were healthy and no dead animals were found in surrounding areas, as had occurred in previous epizootic disease. We performed microscopic and biochemical examinations of the isolates,and compared their whole-genome sequences and transcriptome with those of 10 high virulence Y. pestis strains that were isolated from the adjacent city (Lijiang). We analyzed the phenotypic, genomic, and transcriptomic characteristics of live rodent isolates. The isolates formed a previously undefined monophyletic branch of Y. pestis that was named 1.IN5. Six SNPs, two indels, and one copy number variation were detected between live rodent isolates and the high virulence neighbors. No obvious functional consequence of these variations was found according to the known annotation information. Among the genes that were differentially expressed between the live rodent isolates and their high virulence neighbors, we detected five iron transfer-related genes that were significantly up-regulated in live rodent isolates compared with high virulence isolates (|log2 (FC) | >1, p.adjust <0.05), indicating these genes may be related to the low-virulence phenotype. The novel genotype of Y. pestis reported here provides further insights into the evolution and spread of plague as well as clues that may help to decipher the virulence mechanism of this notorious pathogen.

Dataset Information

Characterization of the mitochondrial genome of the plain flowerpecker, Dicaeum concolor (Dicaeidae) from Yunnan Province, China.

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