Sanger sequencing workshop assessment: identifying sequence X. You must use the technical skills you have acquired during the workshop to determine the identity of the organism from which sequence X is derived. You will find an .ab1 file containing sequence X in the assessment folder (on BB site, Learning Materials/ Sanger sequence analysis/) . This is a gltA (citrate synthase gene) fragment obtained from a putative Bartonella species isolated from the blood of a wood mouse. You should analyse and edit this sequence in Chromas, then transfer it into MEGA and convert it into an appropriate format. You must add this sequence to an alignment of gltA sequence data obtained from 34 of the 35 known Bartonella species for which sequence data are available (the .mas file you need is also in the assessment folder). Note: there are NO sequence data available for the species Bartonella peromysci and Bartonella talpae. You must identify which Bartonella species is missing from the alignment (try here: http://www.bacterio.net/) then find the missing sequence (try here: https://www.ncbi.nlm.nih.gov/pubmed using “Nucleotide” in the drop-down menu to the left of the main search box at the top of the webpage). Once you have found the relevant sequence, you must import it into MEGA, reformat it, and add it to the alignment. Once your alignment is complete, you must use it to generate a dendrogram of relatedness that will demonstrate the species to which the isolate that yielded sequence X belongs. You must present this dendrogram in the form of a Figure, using a format akin to that used in the International Journal of Systematic and Evolutionary Microbiology. The Figure must include an appropriate legend. The Figure must be submitted through Turnitin by 4pm on Tuesday 14th March 2017. Mark scheme (out of 25): 20-25: Perfect or near perfect Figure. Branching order of dendrogram clear and branches well-defined. All branches labelled appropriately with bacterial names in italics, using binomial nomenclature and an appropriate font. All sequences included in the dendrogram in the correct positions, and the architecture of the tree also correct. Appropriate scale included. Legend lucid and succinct containing all necessary information for reader to understand Figure and nothing else. 15-20: Very good Figure, but some errors in terms of its structure, architecture and labelling. All sequences included in the dendrogram. Bacterial names present and almost all correctly presented. Legend lucid and succinct containing most of the information for the reader to understand Figure and little else. 10-15: Good Figure, but some errors in terms of its structure, architecture and labelling and not all sequences included in the dendrogram. Bacterial names present but perhaps not well formatted. Legend present but lacking information most necessary for the reader to understand the Figure. 5-10: Moderate Figure with multiple errors in terms of its structure, architecture and labelling. Several sequences missing from the dendrogram. Bacterial names present but poorly/inconsistently formatted. Legend present by lacking necessary information and/or containing significant amounts of irrelevant information. 0-5: Poor Figure containing numerous errors in terms of its structure, architecture and labelling and many sequences missing included in the dendrogram. Bacterial names incomplete or poorly formatted. No legend, or wholly inadequate legend. B.vinsonii vinsonii B.vinsonii berkhoffii B.vinsonii arupensis B. heixiaziensis B.taylorii B.silvatica B.alsatica B.pachyuromydis B.florencae B.acomydis sequence x B.birtlesii B.koehlerae B.henselae B. senegalensis B.quintana B.callosciuri B.jaculi B.rattaustraliani B.japonica B.coopersplainensis B.queenslandensis B.grahamii B. fuyuanensis B.elizabethae B.tribocorum B.bacilliformis B.rochalimae B.clarridgeiae B. ancashensis B.bovis AF293392.1 Bartonella capreoli GltA (gltA) gene partial cds B.schoenbuchensis B.chomelii B.doshiae B. apis 0.020 http://ijs.microbiologyresearch.org/search?value1=Bartonella+&option1=all&option2=pub_serialIde nt&value2=&operator2=AND
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