Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India.
ICAR Research Complex for NEH Region, Manipur Centre, Imphal, 795004, India.
World J Microbiol Biotechnol. 2021 May 8;37(6):95. doi: 10.1007/s11274-021-03057-8.
Huanglongbing (HLB), also known as 'citrus greening', is an extremely destructive disease of citrus worldwide. HLB is associated with three species of the fastidious proteobacterium, Candidatus Liberibacter asiaticus (CaLas), Ca. L. africanus and Ca. L. americanus with CaLas being the most widely distributed around the world and the only species detected and described so far in India, one of the major global citrus fruit producers. Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. Three types of prophages, Type 1, Type 2 and Type 3 have been identified and described in CaLas so far. In the present study, 441 CaLas isolates sampled across 18 Indian states were used for prophage typing. Based on detection of three prophage types by PCR, all the eight probable combinations of CaLas prophages were identified, including single Type 1 (26.5%), single Type 2 (18.8%), single Type 3 (1.4%), Type 1 + Type 2 (20.4%), Type 1 + Type 3 (12.5%), Type 2 + Type 3 (4.8%), Type 1 + Type 2 + Type 3 (11.3%) and None type (4.3%). Prophage types were confirmed by PCR amplicon sequencing and subsequent phylogenetic analysis. By discovery of all 3 prophages and based on genetic identity and genetic distance, CaLas populations from eighteen citrus growing states were separated into two major Prophage Typing Groups (PTGs): PTG1 and PTG2. The PTG1 comprised of CaLas from North-West India and PTG2 from rest of the country (North-East, Central and South India), and both major groups were further divided into two (PTG1-A, PTG1-B) and three (PTG2-A, PTG2-B and PTG2-C) subgroups respectively. The findings of CaLas population patterns provide evidence for independent origins of HLB-associated CaLas. CRISPR (clustered regularly interspaced short palindromic repeats) array was also detected in CaLas isolates. This is the first report evaluating the genetic variation of a large population of CaLas bacterium in India using the PCR markers from the prophage regions which would certainly assist the ongoing HLB management efforts in India.
黄龙病（HLB），又称“柑橘绿病”，是一种对世界范围内柑橘具有极强破坏性的疾病。HLB 与三种严格的原核生物相关，即 Candidatus Liberibacter asiaticus（CaLas）、Ca. L. africanus 和 Ca. L. americanus，其中 CaLas 在世界范围内分布最广，也是迄今为止在印度唯一检测和描述的物种，印度是全球主要的柑橘水果生产国之一。噬菌体是细菌基因组中高度动态的组成部分，在种内变异中发挥着重要作用。目前已在 CaLas 中鉴定并描述了三种类型的噬菌体，即类型 1、类型 2 和类型 3。本研究使用来自印度 18 个邦的 441 个 CaLas 分离株进行了噬菌体分型。基于 PCR 检测到三种噬菌体类型，鉴定出了 CaLas 噬菌体的所有八种可能组合，包括单一类型 1（26.5%）、单一类型 2（18.8%）、单一类型 3（1.4%）、类型 1+类型 2（20.4%）、类型 1+类型 3（12.5%）、类型 2+类型 3（4.8%）、类型 1+类型 2+类型 3（11.3%）和无类型（4.3%）。通过 PCR 扩增子测序和随后的系统发育分析证实了噬菌体类型。通过发现所有 3 种噬菌体，并基于遗传同一性和遗传距离，将来自 18 个柑橘种植邦的 CaLas 种群分为两个主要的噬菌体分型组（PTG）：PTG1 和 PTG2。PTG1 包括来自印度西北部的 CaLas，PTG2 包括来自印度其他地区（东北部、中部和南部）的 CaLas，这两个主要组进一步分为两个（PTG1-A、PTG1-B）和三个（PTG2-A、PTG2-B 和 PTG2-C）亚组。CaLas 种群模式的发现为 HLB 相关 CaLas 的独立起源提供了证据。还在 CaLas 分离株中检测到了 CRISPR（簇状规则间隔短回文重复序列）阵列。这是首次使用来自噬菌体区域的 PCR 标记评估印度大型 CaLas 细菌种群的遗传变异，这无疑将有助于印度目前正在进行的 HLB 管理工作。
