Background
The genus Citrus and related genera (
Fortunella,
Poncirus,
Eremocitrus, and
Microcitrus) belong to Rutaceae family and subfamily Aurantioideae, which comprise some of the most widely cultivated fruit crops worldwide [
1]. Citrus fruits are rich in various bioactives such as flavonoids, essential oils, carotenoids, limonoids, and synephrines [
2,
3]. These natural nutrients have been reported effective in protecting human from various ailments, including cancer and inflammation, digestive, and cardiovascular diseases. In 2016, Chinese citrus cultivated acreage was 2.56 million hectares, accounting for 27.09% of the world citrus cultivation area. The Chinese citrus annual yield was 35.92 million tons which was 24.53% of the world citrus yield at the same period. Increasing by 27.68% from 2016, by 2022, Chinese citrus cultivated acreage was 45.531 million acres, 1.32 tons/acre for our citrus groves in 2022, orange production in 2022 reached 7.6 million metric tons (
https://www.fas.usda.gov/data/china-citrus-annual-5). Meanwhile, there are abundant wild citrus resources in China, such as
Citrus mangshanensis,
Citrus cavaleriei and
Citrus medica et al. [
3,
4]. But there are still many factors that limit the growth of the citrus cultivation area and production, such as diseases, drought, frigidity, soil salinization, among which citrus tristeza caused by CTV presents as one of the most damaging disasters [
5‐
7].
CTV is a member of the genus
Closterovirus of the family
Closteroviridae, consisting of single-stranded, (+)-sense RNA genome of approximately 19.3 kb in length [
8]. The genome contains 12 open reading frames (ORFs) [
9]. Of these, OFR 7 also known as
p25 gene is 672 bp in length, encoding 97% of the outer coat proteins. The
p25,
p20 and
p23 together function as RNA silencing suppressors [
10]. CTV is mainly transmitted by grafting and aphid vectors, and aphid vector is the most efficient vector of CTV [
11]. One of the most common aphid vectors of CTV is the brown orange aphid (
Aphis citricidus), which has the strongest transmission capacity and can effectively transmit most CTV strains. There are three main symptoms of citrus tristeza disease: quick decline (QD), stem pitting (SP), and seedling yellow (SY). The most common one in China is SP type. Symptoms of SP type include obvious dark brown depression in plant xylem [
5]. Between 1956 and 2000, Spain lost more than 10 million citrus trees because of CTV [
12]. During 1930–2019, CTV destroyed more than 100 million citrus plants in Brazil, Argentina, the United States, Spain, and Israel [
13]. In the late 1980s, China restructured its citrus industry with an increased proportion of honey pomelo, sweet orange, and Shatangju mandarin cultivation, which increased the risk of CTV. Chen et al. [
14] examined 1,439 samples from nine citrus producing areas in China and found that the incidence of CTV was 55.73%.
The molecular characteristics and pathogenesis of CTV as a worldwide disease has been extensively studied, but limited attention has been given to the evolutionary dynamics of this virus, especially regarding its evolutionary dynamics and dispersal patterns in China, studies of the evolutionary dynamics have been reported in rice stripe virus, tomato mosaic virus, infectious bursal disease viruses [
15‐
17]. Silva et al. [
18] used the
p25 gene to estimate the rate of evolution of CTV, and the substitution rate was 1.5 × 10
− 4 subs/site/year (95% credible interval: 1.73 × 10
− 4 subs/site/year − 3.16 × 10
− 4subs/site/year), which proved that CTV was an exceptionally slowly evolving virus. Davino et al. [
19] studied the genetic relationship among CTV strains from Sicily, Italy. The Bayesian phylogenetic analysis revealed that mild and severe CTV isolates belonging to five different lineages were introduced to Sicily in 2002, four lineages co-circulated in Eastern Sicily, one lineage (composed of mild isolates) spread to distant areas of Sicily. Benítez-Galeano et al. [
20] used
p25 genes to infer the substitution rate and spread of CTV-
NC genotypes. Their results showed that the substitution rate of the CTV-
NC genotype was 1.19 × 10
− 3 subs/site/year, the most common recent ancestor appeared in 1977. And the genotype of CTV-
NC was originated from the United States. However, all of these studies mentioned above performed phylogenetic analysis of CTV globally and did not perform Bayesian analysis of CTV in China. Critically, CTV has been found on wild citrus in China [
21,
22], but none of these studies explored whether CTV originated from cultivated or wild citrus. While the study on CTV of evolutionary dynamics and dispersal patterns will give a lot of hints for CTV prevention.
In this study, we collected the CTV-infected citrus samples from several citrus production regions from China, including Sichuan province, Hubei province, Chongqing province, Hunan province, Zhejiang province, Jiangxi province, Fujian province, Guangxi province and Guangdong province, and related publicly available data of CTV were studied in this article. The purpose of this research was (a) determining the distribution of CTV in China, (b) inferring the history of CTV transmission in China, and (c) inferring whether CTV originated from wild or cultivated citrus.
Discussion
In this study, we collected 126 CTV
p25 gene sequences for Bayesian phylogeographic analysis to infer the origin and transmission patterns of the CTV in China. The results showed that there were genetic differences among CTV in China (Fig.
2). CTV was found in all 10 provinces, while, from the overall trend (Fig.
1), CTV is mainly concentrated in the southern and coastal areas of which the geographical location near the Yangtze River Delta, Pearl River Delta, Hong Kong, Macao, Taiwan and Southeast Asia area. And these places located in temperate region. Possible reason to that would be the temperature and climate of these places are suitable for citrus planting, providing ideal host habitats for CTV and the aphids. Besides, these places are suitable for citrus import and export trade, and the accompanied with the import and export of citrus the spread of CTV happened. As reported Pakistan’s citrus exports increased every year (
www.freshplaza.com), and CTV detection rates were also rising. The surveys revealed that the average incidence of CTV in 10 major citrus growing districts in the Northwest of Pakistan steadily increased from 24% (in 2002) to 31%, 35%, 39% and 44% in 2004, 2006, 2008, 2010, respectively [
38]. These evidences indicate that the occurrence and spread of CTV are correlate with the citrus acreage in a degree.
The MCC tree (Fig.
2) showed that the most recent common ancestor of the CTV variant was in 1875 (95% confidence interval: 1676.57 ~ 1961.02), at the same period detected by molecular methods the first by Matsumoto et al. [
39], and the substitution rate of CTV
p25 gene was 4.70 × 10
− 4 subs/site/year (95% confidence interval: 1.10 × 10
− 4 subs/site/year ~ 9.10 × 10
− 4 subs/site/year). Silvan et al. [
18] estimated the substitution rate of CTV
p25 gene was 1.58 × 10
− 4 subs/site/year, and Benítez et al. [
20] estimated the substitution rate of
NC Lineage was 1.19 × 10
− 3 subs/site/year. In this regard, it would be due to Benítez et al. inferred the substitution rate of
NC Lineage only, whereas the study by Silvan et al., many strains were studied, and CTV is mostly mixed infection in the field. And the d
N/d
S value of selective test in this study was 0.05, which was smaller than 1, indicating that CTV was under negative selection. In fact, as the main plant host of CTV, the citrus planting of China was changed in recent years. On the one hand, the large number of foreign introductions and domestic citrus varieties were planted (
http://www.farmchina.org.cn/). As recorded, between 1972 and 2001, 356 citrus varieties were imported from abroad, of which 24 citrus varieties applied in production, like Newhall, Blood orange, Valencia late et al. On the other hand, more and more citrus varieties were crossed after those citruses were introduced, which made the varieties of citrus grown in China increasingly complex. Last decades has witnessed were rapid development of the Chinese citrus industry. Up to 2017, citrus planting acreage had reached 2.60 million hectares (
https://www.fas.usda.gov/data/china-citrus-annual-3). With the growth of species and planting area, the positive rate of CTV increased and pesticide spraying was also increased. As a result, under those evolutionary pressures, such as hosts varieties, genotypes that are more adapted to environments would formatted either.
Along with the migration of citrus seedlings and artificial breeding, CTV dispersal breaks out. Phylogeographic analysis results that CTV originated from wild citrus in HJ, and then spread to cultivated citrus in the SCH, FZ and GG production areas and wild citrus in YN (Fig.
3a). The robustness of these patterns conformed by phylogeographic reanalysis as mentioned in the front section (Materials and Methods). CTV originated from wild citrus in YHJ, and then spread to cultivated citrus in the SCH, FZ and GG production areas (Supplementary Table
2), which emphasized the accuracy of the dispersal patterns of CTV, especially the spread of CTV from the wild to cultivated citrus in the SCH, FZ and GG production area. Divided into 3 stages (Fig.
4), the Bayesian skyline results presented the same clues. The first stage of Bayesian skyline was before 1990, the CTV population size basically remained stable. The second stage was between 1990 and 2005, of which the CTV population size showed an increasing trend. However, as reported that from December 1991 to spring 1992, most citrus production areas, the south of the Yangtze River in China, suffered from cold disasters (
http://www.cma.gov.cn/). As a result, citrus planting area reduced sharply. While, the Bayesian skyline showed that CTV population size was not affected by the cold disasters (Fig.
4), and what’s interest was the population size got an expansion in the following 15 years. The consistent popular of CTV on the one hand, would be due to the host diversity, such as Passiflora [
40] and so on. On the other hand, at the end of the 20th century and early 21th century (
http://www.farmchina.org.cn/), the planting species and acreage in China has increased. These kinds of navel orange imported from abroad accompanied with increasing planting acreage, not only has offset the impact of freezing injury to citrus industry, but also has induced the expansion of the CTV population. The third stage was that after 2005, in this stage, more and more lines such as late maturing navel orange, Orah mandarin, Citrus reticulata ‘Ai Yuan 28’, Citrus reticulata ‘Bu ZhiHuo’ and so on developed rapidly.
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