Protocols for "The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China"
3Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China;
4Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, Yunnan, China
Collection Citation: Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin Liu, Radoje Drmanac, Huan Liu 2020. Protocols for "The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China". protocols.io https://dx.doi.org/10.17504/protocols.io.bjq6kmze
Manuscript citation:
Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin Liu, Radoje Drmanac, Huan Liu, The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China, Gigabyte, 2020 https://doi.org/10.46471/gigabyte.4
License: This is an open access collection distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 14, 2020
Last Modified: August 14, 2020
Collection Integer ID: 40446
Keywords: Extremely Small Populations, draft genome, Nyssa yunnanensis,
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).
We have assembled 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. Protocols used include DNA-extraction, DNA Sequencing using the BGI-SEQ 500 (now known as DNBSEQ-G50) sequencer, and sequencing of 10X linked-reads.
