Phytophthora infestans


Phytophthora infestans[] is an oomycete or water mold, a fungus-like microorganism that causes the serious potato and tomato disease known as late blight or potato blight. Early blight, caused by Alternaria solani, is also often called "potato blight". Late blight was a major culprit in the 1840s European, the 1845–1852 Irish, and the 1846 Highland potato famines. The organism can also infect some other members of the Solanaceae. The pathogen is favored by moist, cool environments: sporulation is optimal at in water-saturated or nearly saturated environments, and zoospore production is favored at temperatures below. Lesion growth rates are typically optimal at a slightly warmer temperature range of.

Etymology

The genus name Phytophthora comes from the Greek φυτόν, meaning 'plant' – plus the Greek φθορά, meaning 'decay, ruin, perish'. The species name infestans is the present participle of the Latin verb infestare, meaning 'attacking, destroying', from which the word "to infest" is derived. The name Phytophthora infestans was coined in 1876 by the German mycologist Heinrich Anton de Bary.

Life cycle, signs and symptoms

The asexual life cycle of Phytophthora infestans is characterized by alternating phases of hyphal growth, sporulation, sporangia germination, and the re-establishment of hyphal growth. There is also a sexual cycle, which occurs when isolates of opposite mating type meet. Hormonal communication triggers the formation of the sexual spores, called oospores. The different types of spores play major roles in the dissemination and survival of P. infestans. Sporangia are spread by wind or water and enable the movement of P. infestans between different host plants. The zoospores released from sporangia are biflagellated and chemotactic, allowing further movement of P. infestans on water films found on leaves or soils. Both sporangia and zoospores are short-lived, in contrast to oospores which can persist in a viable form for many years.
People can observe P. infestans produce dark green, then brown then black spots on the surface of potato leaves and stems, often near the tips or edges, where water or dew collects. The sporangia and sporangiophores appear white on the lower surface of the foliage. As for tuber blight, the white mycelium often shows on the tubers' surface.
Under ideal conditions, P. infestans completes its life cycle on potato or tomato foliage in about five days. Sporangia develop on the leaves, spreading through the crop when temperatures are above and humidity is over 75–80% for 2 days or more. Rain can wash spores into the soil where they infect young tubers, and the spores can also travel long distances on the wind. The early stages of blight are easily missed. Symptoms include the appearance of dark blotches on leaf tips and plant stems. White mold will appear under the leaves in humid conditions and the whole plant may quickly collapse. Infected tubers develop grey or dark patches that are reddish brown beneath the skin, and quickly decay to a foul-smelling mush caused by the infestation of secondary soft bacterial rots. Seemingly healthy tubers may rot later when in store.
P. infestans survives poorly in nature apart from on its plant hosts. Under most conditions, the hyphae and asexual sporangia can survive for only brief periods in plant debris or soil, and are generally killed off during frosts or very warm weather. The exceptions involve oospores, and hyphae present within tubers. The persistence of viable pathogen within tubers, such as those that are left in the ground after the previous year's harvest or left in cull piles is a major problem in disease management. In particular, volunteer plants sprouting from infected tubers are thought to be a major source of inoculum at the start of a growing season. This can have devastating effects by destroying entire crops.

Mating types

The mating types are broadly divided into A1 and A2. Until the 1980s populations could only be distinguished by virulence assays and mating types, but since then more detailed analysis has shown that mating type and genotype are substantially decoupled. These types each produce a mating hormone of their own. Pathogen populations are grouped into clonal lineages of these mating types and includes:

A1

A1 produces a mating hormone, a diterpene α1. Clonal lineages of A1 include:
  • CN-1, -2, -4, -5, -6, -7, -8 – mtDNA haplotype Ia, China in 1996–97
  • – Ia, China, 1996–97
  • – Ia, China, 2004
  • – IIb, China, 2000 & 2002
  • – IIa, China, 2004–09
  • – Ia/IIb, China, 2004–09
  • –, mtDNA haplo Ia subtype, Japan, Philippines, India, China, Malaysia, Nepal, present some time before 1950
  • – Ia, India, Nepal, 1993
  • – Ia, India, 1993
  • JP-2/SIB-1/RF006 – mtDNA haplo IIa, distinguishable by RG57, intermediate level of metalaxyl resistance, Japan, China, Korea, Thailand, 1996–present
  • – IIa, distinguishable by RG57, intermediate level of metalaxyl resistance, Japan, 1996–present
  • – IIa, distinguishable by RG57, intermediate level of metalaxyl resistance, Japan, 1996–present
  • sensu Zhang – IIa, Korea, 2002–04
  • KR_1_A1 – mtDNA haplo unknown, Korea, 2009–16
  • – Ia, China, 2004
  • – Ia, India, Nepal, 1993, 1996–97
  • – Ia, Nepal, 1997
  • – Ia, Nepal, 1999–2000
  • – Ia, Nepal, 1999–2000
  • – Ib, Nepal, 1999–2000
  • – Ib, China, India, Nepal, Japan, Taiwan, Thailand, Vietnam, 1940–2000
  • – Ia, Nepal, 1999–2000
  • – mtDNA haplo unknown, Nepal, 1999–2000
  • – IIb, Taiwan, Korea, Vietnam, 1998–2016
  • – IIb, China, 2002 & 2004
  • – IIa, Korea, 2003–04
  • – Ia, Indonesia, 2016–19

  • A2

Discovered by John Niederhauser in the 1950s, in the Toluca Valley in Central Mexico, while working for the Rockefeller Foundation's Mexican Agriculture Program. Published in Niederhauser 1956. A2 produces a mating hormone α2. Clonal lineages of A2 include:
  • CN02 – See [|#13_A2/CN02] below
  • – with mtDNA haplotype H-20
  • – IIa, Japan, Korea, Indonesia, late 1980s–present
  • sensu Gotoh – IIa, differs from JP-1 by one RG57 band, Korea, 1992
  • – mtDNA haplo unknown, Korea, 2009–16
  • – Ia, China, 2001
  • – Ia, Nepal, 1999–2000
  • – Ib, Nepal, 1999–2000
  • – Ia, Nepal, 1999–2000
  • – Ia, Thailand, China, Nepal, 1994 & 1997
  • Unknown – Ib, India, 1996–2003
  • – Brazil
  • – IIa, Korea, 2002–03
  • /CN02 – Ia, China, India, Bangladesh, Nepal, Pakistan, Myanmar, 2005–19

    Self-fertile

A self-fertile type was present in China between 2009 and 2013.

Physiology

is the in P. infestans. Hosts respond with autophagy upon detection of this elicitor, Liu et al. 2005 finding this to be the only alternative to mass hypersensitivity leading to mass programmed cell death.

Genetics

P. infestans is diploid, with about 8–10 chromosomes, and in 2009 scientists completed the sequencing of its genome. The genome was found to be considerably larger than that of most other Phytophthora species whose genomes have been sequenced; P. sojae has a 95 Mbp genome and P. ramorum had a 65 Mbp genome. About 18,000 genes were detected within the P. infestans genome. It also contained a diverse variety of transposons and many gene families encoding for effector proteins that are involved in causing pathogenicity. These proteins are split into two main groups depending on whether they are produced by the water mold in the symplast or in the apoplast. Proteins produced in the symplast included RXLR proteins, which contain an arginine-X-leucine-arginine sequence at the amino terminus of the protein. Some RXLR proteins are avirulence proteins, meaning that they can be detected by the plant and lead to a hypersensitive response which restricts the growth of the pathogen. P. infestans was found to encode around 60% more of these proteins than most other Phytophthora species. Those found in the apoplast include hydrolytic enzymes such as proteases, lipases and glycosylases that act to degrade plant tissue, enzyme inhibitors to protect against host defence enzymes and necrotizing toxins. Overall the genome was found to have an extremely high repeat content and to have an unusual gene distribution in that some areas contain many genes whereas others contain very few.
The pathogen shows high allelic diversity in many isolates collected in Europe. This may be due to widespread trisomy or polyploidy in those populations.

Research

of P. infestans presents sampling difficulties in the United States. It occurs only sporadically and usually has significant founder effects due to each epidemic starting from introduction of a single genotype.

Origin and diversity

The highlands of central Mexico were considered to be the center of origin of P. infestans, although others have proposed its origin to be in the Andes, which is also the origin of potatoes. A study published in 2014 evaluated these two alternate hypotheses and found conclusive support for central Mexico being the center of origin. However, their study did not include either an extensive global sampling of P. infestans or historic genomes. Support for a Mexican origin specifically the Toluca Valley came from multiple observations including the fact that populations are genetically most diverse in Mexico, late blight is observed in native tuber-bearing Solanum species, populations of the pathogen are in Hardy–Weinberg equilibrium, the two mating types occur in a 1:1 ratio, and detailed phylogeographic and evolutionary studies. For instance, while sexual recombination is regarded as evidence for a Mexican origin, P. infestans is mostly asexual and does not widely engage in sexual reproduction, despite the migration of the A2 mating type into Europe. Furthermore, the sister lineages of P. infestans, namely P. mirabilis and P. ipomoeae are endemic to central Mexico.
Others have proposed an Andean origin for Phytophthora infestans. In 2002, Ristaino assessed the evidence for both the Mexican and South American origin hypotheses . She pointed to the absence of potato exports during the 1840s, which posed a challenge to the notion of a Mexican origin for the blight's migration to the US and Europe . Furthermore, historical accounts of a similar disease in the Andean region and the presence of the cosmopolitan US-1 lineage in South America since at least the 1980s were invoked by Ristaino, potentially supporting the idea of a South American origin . In 2016, the Ristaino lab with collaborators Mike Martin and Tom Gilbert, at the University of Copenhagen, conducted the largest whole genome sequencing project to date with historic and modern day lineages of P infestans. Analysis of these  more extensive genomic dataset that included both P. infestans and P. andina isolates documented an  Andean origin of the species . Lineages of Andean origin were found to be more closely related to historical P. infestans lineages from the famine era, implying an Andean origin with later subsequent migration and diversification occurring in Mexican lineages . Significant admixture between the historic P infestans and P andina was also documented . Several close relatives of P infestans have been found in the Andes in South America, including P. andina, P urerae and P betacei.
Coomber et al., examined the evolutionary history of Phytophthora infestans and its close relatives in the 1c clade using whole genome sequence data from 69 isolates of Phytophthora species in the 1c clade and conducted a range of genomic analyses including nucleotide diversity evaluation, maximum likelihood trees, network assessment, time to most recent common ancestor and migration analysis [26