• Thesis: Phylogenomics reveals genetic mechanism in adaptive radiation of Melastoma
• Supervisor: Dr. Renchao Zhou
• Average Score: 90.94/100
• Expected Graduation Time: July 2023

• Thesis: Phylogeography and ecological adaptability of Allium forrestii and A. changduense
• Supervisor: Dr. Xingjin He
• GPA: 3.85/4.0; Average Score: 90.82/100

• GPA: 3.21/4.0; Rank: 2/32

• Genomic evolution of Melastoma candidum and comparative genomics analysis with M. dodecandrum.
• Genetic mechanism of adaptive radiation of Melastoma with Indo-West Pacific distribution.
• Genetic mechanism of flower color variation in Melastoma malabathricum.
• Genomic evolution and genetic diploidization of the homosporous fern Adiantum nelumboides.
• Allopolyploidy origin and genetic mechanism of flower color variation in the legume Bauhinia variegate.
• Evolutionary studies of the organelle genomes of plants, including the parasitic plants Aeginetia indica, Rhopalocnemis phalloides, and the mangrove fern Acrostichum aureum, and so on.

• Genetic diversity and phylogeographic research of Allium forrestii and A. changduense based on one nuclear DNA sequence (ITS) and three chloroplast DNA sequences (atpI-atpH, trnL-trnF and ndhC-trnV) in the population level.

Biological Computer Programming Languages                                         Sun Yat-sen University, Fall 2020
Molecular Biology                                                                                 Sun Yat-sen University, Spring 2020

Maintenance and administration of two servers and over 30 users

• Genome assembly and annotation with long reads and short reads: Canu, Nextdenovo, maker-P, EDTA, repeatmasker, repeatmodeler, etc.
• Genome evolution analysis including SVs, SNPs, WGD, pseudogene identification, gene family analysis based on MCScanX, jcvi, MUMmer, CAFÉ5, etc.
• Identification of trait-determining candidate genes using QTL-seq and transcriptome.
• Phylogeny and divergence time dating based on NGS data with GATK, IQ-TREE, RAxML-NG, PAUP, BEAST, MrBayes, PAML, OrthoFinder2, etc.
• Gene flow and introgressive analysis based on Dsuite, PhyloNetworks, TreeMix, etc.
• Biogeographic analysis with Maxent, DIVA-GIS, etc.
• Plant organelle genome assembly and annotation.
• Plant organelle evolution analysis including HGT, IGT, pseudogenes, rearrangement, etc.

• Linux: bash scripts, text processing tools, server maintenance, etc.
• Languages: R, Python

• DNA extraction and PCR amplification
• Sanger sequencing, and genome, transcriptome, organelle genome sequencing
• Root apical cell chromosome count
• Microorganism isolation and purification

• Plant hybridization experiments
• Herbarium specimen preparation and identification
• Field sampling in Hengduan Mountains, Tibet, South China and Northern China
• Experience of plant taxonomy in Southwest China

• blog address: https://yanzhongsino.github.io
• published over 80 blogs related to bioinformatics analysis and biological evolution and genetics research methods.
• also published on WeChat Public, the most popular blogging platform in China

• The Second-grade Scholarship in Sun Yat-sen University
• The First-grade Scholarship in Southwest University

• 2022, oral presentation (in English). Plant Genomes Online (PGO). April 27-28, 2022, online. “Chromosomal-level genome assembly of the orchid tree Bauhinia variegata supports the allotetraploid origin hypothesis of Bauhinia”. https://www.youtube.com/watch?v=ltTRYpB9VeY.
• 2020, participation. Annual Conference of Guangdong and Guangxi Botany Association, December 17-19, 2020, Shenzhen, China, Hosted by Guangdong and Guangxi Botany Association.
• 2019, participation. Annual Conference of Guangdong Botany Association, December 21, 2019, Dongguan, China, Hosted by Guangdong Botany Association.
• 2019, participation. The 3rd Natural Hybridization and Biodiversity Conference, October 25-27, 2019, Kunming, China, Hosted by Biodiversity Committee of Chinese Academy of Sciences and Yunnan Wu Zhengyi Science Foundation.

• 2022. Summer Camp on Frontier Ideas and Methods in Evolutionary Biology, August 01-12, 2022, online, Hosted by Human Population Omics Group at Fudan University, rated as outstanding student and participated in the student presentation. https://pog.fudan.edu.cn/#/conf.
• 2020. The 2nd Workshop and Advanced course on pupulation genetics and genomics, online, September 21-24, 2020, Hosted by Institute of Microbiology, Chinese Academy of Sciences.

1. Yan Zhong, Runxian Yu, Jingfang, et al. (2022). "Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica." Frontiers in Plant Science.
2. Yan Zhong#, Yongbo Liu#, Wei Wu, et al. (2022). "Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides." Genome Biology and Evolution 14(8):1-13.
3. Yan Zhong#, Yong Chen#, Danjing Zheng, et al. (2022). "Chromosomal-level genome assembly of the orchid tree Bauhinia variegata supports the allotetraploid origin hypothesis of Bauhinia." DNA research 29(2):1-9.
4. Yan Zhong, Runxian Yu, Yongmei Chen, et al. (2020). "The complete chloroplast genomes of the mangrove fern Acrostichum aureum." Mitochondrial DNA Part B 5(3): 2258-2259.
5. Runxian Yu, Chenyu Sun, Yan Zhong, et al. (2022). "The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides." Current Biology 32:470-479.
6. [manuscript] Yan Zhong, et al. "Chromosomal-level genome assembly of Melastoma candidum provides some insights into trichome evolution."
7. [manuscript] Yan Zhong, et al. "Phylogenomics of the genus Melastoma reveals the role of natural hybridization in adaptive radiation of Melastoma".
8. [In preparation] Yan Zhong, et al. "Genomic and transcriptomic analysis of flower color variation in Melastoma malabathricum".

1. Yan Zhong, Bin Wang, Jiazhen Zhang, et al. (2018). Pternopetalum porphyronotum (Apiaceae), a new Critically Endangered species with abaxially purple leaflets from Sichuan, China. Nordic Journal of Botany 36(4).
2. Yan Zhong, Yan Yu, Dengfeng Xie, et al. (2018). "Genetic variation and niche differentiation of Allium forrestii and Allium changduense. " Chinese Journal of Ecology 37(4):994-1002.
3. Chuan Xie, Dengfeng Xie, Yan Zhong, et al. (2019). "The effect of Hengduan Mountains Region (HMR) uplift to environmental changes in the HMR and its eastern adjacent area: Tracing the evolutionary history of Allium section Sikkimensia(Amaryllidaceae) ". Molecular Phylogenetics and Evolution 130:380-396.
4. Minjie Li, Dengfeng Xie, Chuan Xie, Yiqi Deng, Yan Zhong, et al. (2019). A Phytogeographic Divide Along the 500 mm Isohyet in the Qinghai-Tibet Plateau: Insights From the Phylogeographic Evidence of Chinese Alliums (Amaryllidaceae). Frontiers in Plant Science 10.