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载，但对于野生环境中的细菌性病原体，尤其是宿主转换期间及转换后的演化速率，学界认知仍较为有限。鸡毒支原体（Mycoplasma gallisepticum, MG）是一种主要在家禽中演化的致病性细菌，近期成功跨宿主传播至野生家朱雀（*Carpodacus mexicanus*，北美常见鸣禽）。本研究首次对感染家朱雀的MG分离株及其家禽外类群菌株进行基因组解析，并测算其基因组演化速率。研究利用13年连续采样获得的12株家朱雀MG分离株的全基因组序列，以及新增测序的4株家禽MG菌株，测算得到：家朱雀分离株的核苷酸多样性仅约为其祖先家禽菌株的2%；家禽与家朱雀群体的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。我们还发现，在跨宿主传播至家朱雀之前，家禽MG菌株的成簇规律间隔短回文重复序列（Clustered Regularly Interspaced Short Palindromic Repeats，CRISPR）阵列具有高度多样性且发生了完全的序列更新；而在成功侵染家朱雀后，CRISPR重复序列的多样性逐渐丧失，且不再招募新的CRISPR重复序列。2007年采集的家朱雀MG菌株仅保留了1994-1995年奠基菌株约50%的CRISPR序列库，且已丧失CRISPR功能所需的CRISPR相关基因。本研究结果表明，野生鸟类细菌性病原体的基因组演化速度可以极快，且在本案例中伴随CRISPR功能的显著丧失。