Initial notes on species selection
This file contains a list of the species selected for assembly pull down from NCBI Assembly database, plus the reasoning behind their selection (incluidng references).
LP: An additional criterion to consider would be which species/isolates can we get material for. Phytophthora is a shoo-in, as are Magnaporthe/Pyricularia spp.
Plant pathogens Evidence of microorganism being a plant pathogen in the literature. Reasoning: to be a plant pathogen the microorganism must be able to invade the host plant cells, and thus must be able to pass through the plant cell wall, indicative that the may do by expressing and secreting extracellular plant cell wall degrading enzymes (Chiapello et al., 2015; Kamoun et al., 2015)
LP: in your draft thesis section, it would be useful to have a figure illustrating the typical ways in which fungi/oomycetes penetrate the plant, highlighting the points that PCWDEs would be useful.
Some species have been included in genomic analysis experiments to identity novel enzymes and annotate their respecitve genomes, especially those of the Aspergillus genus, however, no studies examning the sequence/phenotype relationship, and especially no literature looking for a common basis with functional variation.
LP: In the draft thesis section, definitely include references to the genome analyses. Maybe better to refer to an area being "underexplored" or "relatively underreported" than blankly stating "no literature" (which is easier to refute with a single reference)
Aspergillus, Trichoderma and Penicillium species Aspergillus, Trichoderma and Penicillcium species have been previously well studied for their biomass degrading behaviours/phenotypes, including studies identifying specific extracellular plant cell wall degradaing enzymes that mediate this behaviour (Weinmann et al., 2013) - many of these species from these gensuses could be a good source of plant cell wall degrading enzymes.
Trichoderma have been shown to utilise a diverse range of carbon sources, showing potential to degrade a range of plant cell wall polysaccharides, and are often used in biotechnological apllications owing to their ability to convert plant biomass into soluble sugars which are suitable for fermentation into biofuel (Kubicek and Druzhinina, 2013) ++ lack of genomic computational studies studying many Trichoderma spp.
LP: good initial summaries - a couple more references would be helpful in the draft thesis section
Rhynomodosporium and Magnaporthe species Rhynomodosporium and Magnaporthe genuses contain many plant pathogens (reference needed), indicative of possing extracellular plant cell wall degrading enzymes.
LP: Do you mean Rhynchosporium (as in the references)? I've not heard of Rhynomodosporium.
King et al., 2013 - Rhynchosporium commune, R. agropyri and R. secalis are all closely related, thus good for homology study (reference from else where)
One of the most used fungal species in industry. Well studied and utilised in industry for its enzyme-driven biomass degradation, speficically being shown to possess high lignocellulosic material degradation efficiency (Kubicek and Druzhinina, 2013; Horta et al., 2018; Paula et al., 2018).
Additionally, the species has been shown to survive off a diverse range of biological substrates, numerous times, indicating a repertoire of enzymes that can target a diverse range of polysaccharides(Horta et al., 2018; Paula et al., 2018), thus increasing the potential of identifying cazymes from this species that can degrade one or multiple plant cell polysaccharides.
Trichoderma citrinovirde, Trichoderma harzianum, Trichoderma atrovidide and Trichoderma pseduokoningii
Demonstrated degradation of sawdust biomass (Kim et al., 2019) - sawdust from forestry industry can be used as feedstock for biofuel, thus demonstrating excellent potential for source of biocatalysts for biofuel production.
Kim et al., 2019: Tested using clearance zones in petri dishes, using different biolgoical substrates as carbon source. Tested for:
- beta-glucosidase
- avicelase
- CM-cellulase
- amylase
- pectinase
- xylanase
N = 1 for each test, thus cannot perform statilstical analysis to determine relative levels of degradation activity therefore, all four species selected as potential sources of plant cell wall degrading enzymes with good engineering potential.
LP: My view is that the literature reference is justification enough. The "N=1" stuff isn't necessary.
T. citrinovidie Biomass degrading xylanase from T citrinovidie has also been used in chicken feed experiments induce biomass degradation to facilitate digestion of the feed by chickens (Lee et al., 2018) - indicates the ability to generate recombinant enzymes from T. citronidie that can be used in isolation and not part of a large enzyme mix, and thus indicates suitability for extracellular biofuel feedstock pre-treatment/saccharification.
T. citrinovide and T.harzianum Shown to degrade mushrooms (Kim et al., 2016) - double check what the study found
T.harzianum Kubicek and Druzhinina, 2013 - T.harzianum are well studied for antifungal (mushroom) pest control, indicates secretion of extracellular Cazyme secretion.
Horta et al., 2018 - demonstrated extracellular cellulase, xylanase and beta-glucosdiase activity of Trichoderma harzianum
Li et al., 2019 - specifically identified LZ117 extracellular cellulase and trialed successful in biomass degradation
Trichoderma atrovirdie Horta et al., 2018 - demonstrated extracellular cellulase, xylanase and beta-glucosdiase activity of Trichoderma atrovirdie
Wang _et al., 2017 - Demonstrated high cellulase, CMCase, FPase and beta-glucosidase activity of T.asperellum T1 strain, and showed ability of T1 to ferment biomass without pretreatment - indicates can breadkown biomass material efficiently - also if can already ferment would facilitate co-/simultaneous sacchrification and fermetnation which is the direction industry wants to move into to increase economic efficienty of biofuel production process.
Wang et al., 2015 - earlier work of the Wang et al., 2017 paper showing high efficiency of T1 to degrade lignocellulisic biomass.
Magnaporthe oryzae (anamorph: Pyricularia oryzae) and Magnaporthe grisea (anamorph: Pyricularia grisea)
Note: for this species use its anamorph name for NCBI, although NCBI does seem to autmatically correct for this, then still note that a different name will appear instead of 'Magnaporthe oryzae'
Magnaporthe grisea Magnaporthe oryzae
LP: Ah - I see you're handling the nomenclature issue, here. That's good - see the note in the species list, and use Pyricularia in there.
Dean et al., 2012 - Voted top plant pathogen in 2012 in Molecular Plant Pathogen journal ++ supported by Shirke et al., 2016 - "Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets."
LP: If you wanted a bit more background for "colour" in your thesis draft, this paper leads to interesting places: https://www.nature.com/articles/nature10947 - don't forget to check for papers that cite it, as well as those cited by it, when you do a literature search
Dean et al., 2012 - Voted second plant pathogen in 2012 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted fourth plant pathogen in 2012 in Molecular Plant Pathogen journal - damaging most typically cereal crops
Dean et al., 2012 - Voted fifth plant pathogen in 2012 in Molecular Plant Pathogen journal - diverse range of plant hosts cotton, tomato to bananna plants.
Dean et al., 2012 - Voted sixth plant pathogen in 2012 in Molecular Plant Pathogen journal - also cereal crop host
Dean et al., 2012 - Voted seventh plant pathogen in 2012 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted ninth plant pathogen in 2012 in Molecular Plant Pathogen journal
Fatme et al., 2018; Kao et al., 2019 - used in biofuel production already as organisms and enzymes derived from these species.
Miao et al., 2015 - "Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases and pectinases involved in lignocellulosic biomass degradation."
Gouvea et al., 2018 - "A. fumigatusplaysan important role in plant biomass degradation capabilities and recycling" and demonstrated cellulase, endo-1,4-beta-xylanse and endo-1,3-beta-glucanase activities
Cong et al., 2017 - demonstrated species ability to express lignin peroxidase and manganese perosidase enzymes, and high through put sequencing identifed other CAZymes (17 cellulase and 19 feruloyl esterases that are linked to lignocellulse degradation)
Avrova and Knogge, 2012 - fungal plant pathogen, typically affecting cereal crops ++ supported by King et al., 2013
King et al., 2013 - can breakdown and utilise bearded crouch-grass (agropyron canninum) and couch-grass (Agropyron repens) as carbon source indicating ability to express and secrete extracellular plant cell wall enzymes and thus degrade the plant, causing leaf blotch and allowing the fungi to survive.
King et al., 2013 - same explanation as R. agropyri but in this case survives on rye and triticale ++ supported by Ilyas et al., 2014 - "is a common and widespread disease of barley ... Yield losses up to 45% have been observed due to this fungal disease causing leaf senescence and a reduced number of grains per ear"
Shirke et al., 2016 - "The pure cultures of the Magnaporthe isolates from rice and non-rice host plants were obtained from blast infected leaf and neck tissues using water agar based single spore isolation method. ... The MG03 ... and MG12 were isolated from infected leaf and neck of tissues of finger millet (Eleusine coracana L. Gaertner) varieties Uduru Mallige (MG03 from leaf tissue, MG04 from neck tissue) and PR202 (MG12 from leaf tissue). Similarly, MG05 and MG08 were isolated from infected leaf tissues of foxtail millet and MG07 from buffel grass (Cenchrus celiaris L.)." - basically "Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets" so they took isolates of Magnaporthe species and analysed their genomes, and these are MG03, MG05, MG07, MG08 and MG12 becuase they were shown to be plant pathogens.
Dean et al., 2012 - Voted top oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted joint second oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted joint second oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted fourth oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted fifth oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted sixth oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted seventh oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted joint eighth oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted joint eighth oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
Dean et al., 2012 - Voted tenth oomycete plant pathogen in 2014 in Molecular Plant Pathogen journal
These page contain the initial plans and development notes for pyrewton