Data from: Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum

Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ~2% of ancestral poultry strains and a nucleotide substitution rate of 0.8 – 1.2 X 10-5 per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches, there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ~50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.基因组演化的可量化速率在人类病原体中已有充分记录，但对于野生环境中的细菌病原体而言，相关认知仍较为匮乏，尤其是在宿主切换期间及切换完成后。鸡毒支原体（Mycoplasma gallisepticum, MG）是一种主要在家禽中演化的致病菌，近期成功跨宿主传播至北美常见鸣禽——家朱雀（Carpodacus mexicanus）。本研究首次针对家朱雀分离的MG菌株开展基因组特征解析，并量化其基因组演化速率，同时以家禽来源的MG菌株作为外类群进行对照分析。本研究利用13年间连续采集的12株家朱雀MG菌株的全基因组序列，以及新增测序的4株家禽MG菌株，经分析估算：家朱雀分离株的核苷酸多样性仅约为祖先家禽菌株的2%；且无论在家禽还是家朱雀群体中，核苷酸替换速率均为0.8–1.2×10^-5 每个位点每年，这一速率极快，可与目前已报道的部分细菌最高替换速率相媲美。研究同时发现，在跨宿主切换至家朱雀之前，家禽MG菌株的CRISPR（Clustered Regularly Interspaced Short Palindromic Repeats）阵列具有高度多样性且完全更新；而在入侵家朱雀宿主后，CRISPR重复序列多样性逐渐丧失，且不再招募新的CRISPR重复序列。2007年新近分离的家朱雀MG菌株仅保留了1994-1995年奠基菌株约50%的CRISPR序列库，且丢失了CRISPR功能所需的相关基因。本研究结果表明，野生鸟类致病菌的基因组演化速度可能极快，而在本案例中，这一演化过程伴随了CRISPR的功能性丧失。