Dataset Information

The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China.

ABSTRACT: Nyssa yunnanensis is a deciduous tree species in the family Nyssaceae within the order Cornales. As only eight individual trees and two populations have been recorded in China's Yunnan province, this species has been listed among China's national Class I protection species since 1999 and also among 120 PSESP (Plant Species with Extremely Small Populations) in the Implementation Plan of Rescuing and Conserving China's Plant Species with Extremely Small Populations (PSESP) (2011-2-15). Here, we present the draft genome assembly of N. yunnanensis. Using 10X Genomics linked-reads sequencing data, we carried out the de novo assembly and annotation analysis. The N. yunnanensis genome assembly is 1475 Mb in length, containing 288,519 scaffolds with a scaffold N50 length of 985.59 kb. Within the assembled genome, 799.51 Mb was identified as repetitive elements, accounting for 54.24% of the sequenced genome, and a total of 39,803 protein-coding genes were predicted. With the genomic characteristics of N. yunnanensis available, our study might facilitate future conservation biology studies to help protect this extremely threatened tree species.

SUBMITTER: Mu W

PROVIDER: S-EPMC9632040 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China.

Mu Weixue W Wei Jinpu J Yang Ting T Fan Yannan Y Cheng Le L Yang Jinlong J Mu Ranchang R Liu Jie J Zhao Jianming J Sun Weibang W Xu Xun X Liu Xin X Drmanac Radoje R Liu Huan H

GigaByte (Hong Kong, China) 20200801

Nyssa yunnanensis is a deciduous tree species in the family Nyssaceae within the order Cornales. As only eight individual trees and two populations have been recorded in China's Yunnan province, this species has been listed among China's national Class I protection species since 1999 and also among 120 PSESP (Plant Species with Extremely Small Populations) in the Implementation Plan of Rescuing and Conserving China's Plant Species with Extremely Small Populations (PSESP) (2011-2-15 ...[more]

PMID: 36824597

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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

The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China.

Publications

The draft genome assembly of the critically endangered <i>Nyssa yunnanensis</i>, a plant species with extremely small populations endemic to Yunnan Province, China.

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