[Latest Research Progress] Breakthrough Research Published on Molecular Biology and Evolution

　　 　　

Recently, Professor Jiang Yu's team has made an important breakthrough in the study of chicken pan-genome. The research paper "De novo assembly of 20 chicken genomes returns the undetectable phenomenon for thoughts of core genes on micro-chromosomes and sub-telomeric regions" was published in  Molecular Biology and Evolution . Li Ming, Ph.D. student of the college, Sun Congjiao, associate professor of China Agricultural University, Xu Naiyi and Bian Peipei, graduated master Tian Xiaomeng, Wang Xihong, associate professor of the college, and Wang Yuzhe, teacher of China Agricultural University, are the co-first authors of this article. Professor Yang Ning of China Agricultural University, Professor Jiang Yu of College and Professor Hu Xiaoxiang of China Agricultural University are co-correspondents.

The research results decrypted the "black box" of poultry genome, and contributed to the development and improvement of chicken and even bird genome. In this study, the model animal of birds-chickens was taken as the research object, and the first high-quality pan-genome based on de novo assemblies was constructed by assembling the genomes of 20 individuals from 15 domestic chicken breeds worldwide. Although domestic chickens already have the best reference genome in birds, researchers still found the missing sequence of reference genome equivalent to 15% (159 MB) of the current reference genome. It is worth noting that these reference genome deletion sequences include 1335 protein coding genes and 3011 lncRNA genes. Compared with a large number of deletion sequences/genes found in plant pan-genome, which are non-core sequences (only exist in some individuals), most of the deletion sequences/genes found in chicken reference genome in this study are core sequences/genes. Through the systematic screening, the authors found that the number of genes in birds can reach the same level as that of other tetrapods, which greatly updated our understanding of bird evolution.

Small chromosomes are the most noticeable feature of bird genome. Previous studies have shown that small chromosomes of birds have the characteristics of high GC content, high tandem repeat (TR) content, high recombination rate and high gene density. By genomic mapping of these deletion sequences/genes in the reference genome, the authors found that they mainly congregate in the subtelomeric regions of small chromosomes and large chromosomes with similar traits to small chromosomes. Further analysis shows that the proportion of TR contained in these deletion sequences is amazing. The TR ratio of human subtelomere region is 2.2%, while 79% of novel sequences in chicken subtelomere region are TR, and the rest are filled with exons. A high proportion of TR contains G4 motif, forward repeat and mirror repeat, which can form dynamic nonclassical DNA secondary structure in different individuals, thus preventing the smooth progress of sequencing.

Number of protein coding genes in representative species of mammals, reptiles and birds

Collinearity analysis of newly discovered coding gene on chicken chromosome 16 with human, lizard, turtle and thrush

This study also found that the replacement rate of missing genes in the newly discovered reference genome is 3 times higher than that of known genes, which updates people's understanding of bird evolution rate. Moreover, most of these reference genome deletion genes have been confirmed to be shared in all chicken genomes, including many housekeeping genes, and enriched in immune pathways. However, the evolutionary strategy of concentrating a large number of functional genes with high substitution rate on small chromosomes and subtelomeric regions of large chromosomes has an impact on highly evolved branches (dinosaur-bird branches) in the past 250 million years, which deserves further exploration. This study provides an example for the perfection of bird genome, which will significantly affect the evolution and comparative genomics of birds. At the same time, the pan-genome resources of chickens provided by this study will also provide powerful assistance for genetic breeding and functional gene mining of domestic chickens.