From 61c504ec61b600325002cee47d5029014f2d0010 Mon Sep 17 00:00:00 2001 From: Samuel Ortion Date: Tue, 26 Mar 2024 15:16:00 +0100 Subject: [PATCH] feat: Adding some text on duplication mechanisms --- .gitattributes | 1 + Makefile | 3 +- figures/lallemand2020-fig1_copy.pdf | 3 + figures/lallemand2020-fig1_copy.svg | 438 ++++++++++++++++++++++++++++ glossary.tex | 1 - main.pdf | 3 - media/logo/logo-lamme.pdf | Bin 4360 -> 129 bytes media/logo/logo-psaclay.pdf | Bin 3670 -> 129 bytes media/logo/logo-ueve.pdf | Bin 9799 -> 129 bytes report.org | 88 ++++-- report.pdf | Bin 68780 -> 131 bytes report.tex | 100 ++++++- sty/lamme2024.sty | 13 + sty/test_figurelefttextright.pdf | Bin 24048 -> 130 bytes titlepage.tex | 7 +- 15 files changed, 622 insertions(+), 35 deletions(-) create mode 100644 figures/lallemand2020-fig1_copy.pdf create mode 100644 figures/lallemand2020-fig1_copy.svg delete mode 100644 glossary.tex delete mode 100644 main.pdf diff --git a/.gitattributes b/.gitattributes index defcde4..af51b13 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,2 @@ main.pdf filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text diff --git a/Makefile b/Makefile index 0011af3..8fbc493 100755 --- a/Makefile +++ b/Makefile @@ -1,6 +1,5 @@ OPTIONS=-shell-escape -file-line-error -synctex=1 -SOURCE=main - +SOURCE=report all: latexmk bib glossaries latexmk build: diff --git a/figures/lallemand2020-fig1_copy.pdf b/figures/lallemand2020-fig1_copy.pdf new file mode 100644 index 0000000..70b33c6 --- /dev/null +++ b/figures/lallemand2020-fig1_copy.pdf @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6715675aa7948682339b7d77f4e1649e4aa887ad98f51be638a5463043697094 +size 18041 diff --git a/figures/lallemand2020-fig1_copy.svg b/figures/lallemand2020-fig1_copy.svg new file mode 100644 index 0000000..be19c31 --- /dev/null +++ b/figures/lallemand2020-fig1_copy.svg @@ -0,0 +1,438 @@ + + + + + + + + + + + + + + A + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + whole genome duplication + + + B + unequal crossing-over + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/glossary.tex b/glossary.tex deleted file mode 100644 index 170d62b..0000000 --- a/glossary.tex +++ /dev/null @@ -1 +0,0 @@ -\newabbreviation{TAG}{TAGs}{Tandem Arrayed Genes} diff --git a/main.pdf b/main.pdf deleted file mode 100644 index 01b837f..0000000 --- a/main.pdf +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:dca9b524bd8bc8181e650b4e88a811daf768f03127bc5b1c7a7c9638fcc9970c -size 64263 diff --git a/media/logo/logo-lamme.pdf b/media/logo/logo-lamme.pdf index 1956eb075394dd7c82bb47dced364970129a3c4a..e3bfbf12ffc19f8d92766610a9313d779413ff74 100644 GIT binary patch literal 129 zcmWN^$q~aK3;@7CRnS1pAz2`I!x@-KVo$(+r26=^vsd|!zJFw!^B9{_&pscoI+ojZ z#wG1$Vj$giq;!u_HOmW Mj>PD{A`wW7Kc*!nHUIzs literal 4360 zcma)A2Q*w=*PhXhHi!}t#xT*D(R*)$Ac*iP8NK&jGy0II2@=r_B1DPadx#Q=9)t-J z(V`>>BL0!L{O?-d`v3Lab=Ns(pL6y;d#~p?cdh5b4Ae9P5klf1Si?@$8AuEQhj`k! 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They have a particular role in genome evolution, allowing species to explore new gene functionality offering a pool of usable genes to build on. +TODO: +#+end_abstract #+begin_center -duplicate genes, tandem arrayed genes, pipeline - +*keywords*: duplicate genes, tandem arrayed genes, pipeline #+end_center +#+begin_export latex +\tableofcontents +#+end_export + +[[printglossaries:]] + +#+begin_export latex +\pagenumbering{arabic} +#+end_export * Context -** Duplicate genes -*** Duplication mechanism +** What are duplicate genes? +Duplicate genes are genes that experienced a duplication event during species evolution. + +These are homologous genes. + +*** Duplication mechanisms +#+name: fig:gene-duplication-mechanisms +#+CAPTION: Mechanisms leading to gene duplication +[[./figures/lallemand2020-fig1_copy.pdf]] +Several mechanisms may lead to gene duplication. We review them in this section. +**** Segment duplication +**** Retroduplication +Transposable elements cause an important part of gene duplication [citation needed] +Retrotransposon, or RNA transposon is one type of transposable element. Some of the representant of retrotransposon are similar to retroviruses. +Retrotransposon may be duplicated in the genome through a mechanism known as "copy-and-paste". +These transposons are typically composed of a reverse transcriptase gene. The protein encoded by this gene may proceed in the reverse transcription of the RNA transcript of the transposon sequence resulting in a DNA sequence which can then be included elsewhere in the genome. +During this process, the RNA transcript may include nearby gene sequence, which can thus be copied and pasted along with the retrotransposon. +**** Transduplication +DNA transposon is an other type of transposable element whose transposition mechanisms can lead to gene duplication too. +This type of transposable element moves in the genome through a mechanisms known as "cut-and-paste". +The typical DNA transposon contains a transposase gene. The protein encoded by this gene recognize two sites surrounding the donnor transposon sequence in the chromosome resulting in a DNA cleavage. The transposase can then insert the transposon in a new place of the genome. +Similarly to retrotransposon, if a gene was present between the two cleavage sites of the donnor transposon, it may move with the transposed sequence. +**** Tandem Duplication +**** Polyploidisation +***** Alloployploïdisation +***** Autopolyploïdisation +***** Mechanisms +****** Polyspermy +****** Non-reduced gametes +**** Unequal crossing-over +A crossing-over may occur during cell division. A fragment of chromosome is exchanged between two chromatids of a pair of chromosome. If the cleavage of the two chromatids occured at different positions on both chromosomes, the shared fragments may have different lengths. When the repair of missing fragment is performed, the resulting chromosome will incorporate a duplicate region of the chromosome, leading to a potential duplication for genes present in this region, as represented in figure [[fig:gene-duplication-mechanisms]] B. # TODO: check that this is really the B subfigure *** Role in genome evolution ** Identification of duplicate genes -** FTAG Finder, a method to identify Families and Tandem Arrayed Genes +*** +*** Finder + * Objectives +** Amend the existing Galaxy pipeline +Last year, a M1 student, Seanna Charles, worked on the Galaxy's version of the gls: Finder pipeline [cite:@charlesFinalisationPipelineFTAG2023]. +During my internship, I will continue this work. +** Porting Finder pipeline on a workflow manager -* Tips :noexport: - -To export: -C-c C-e C-b l l +#+begin_export latex +\printbibliography +#+end_export diff --git a/report.pdf b/report.pdf index 095f2410b95d724ea247fc2e7fb052b1a7679ed1..4641ddbe282e67aebb237e43decaca40b9f1039d 100644 GIT binary patch literal 131 zcmWN?!4U!>3;@7CRnUM30fBJcL|%rQx-?p%GXnHXtL=!Ppv>mlwz&Ze{Cg z=KS|+YvgJsYG&eKY6fJGHM6&HwFEM;v9JUA`GNm-z`D3Pn;F@`dTx|xPTS*g!1vs! zoIn#KytN9`b6p!r}g*?NEhX4)h>dC@vXpTDt@(-;xdF$_Q84tCSuUIz;_4TPhQBRy}aEFO%> z>9nLAi_Z@0XCH?{Zfy~5qe9B0Tvp^zo{AdzXtaGjQu(RtYv(%g%8IF!yC>d58sLTiURSaAFcIo{sbVbS!OSJWqbCcseBK=fE-27mHzmcwH15 z3IJFhp>Ubs+tAV-b)_)6$45}npp9iPG`XR7Fw9Gj3*#_Y*|AT?j+GgyVS~+!I;8cX zXW>fa-`&A2A`(RK#nPmM@;H90^2*_)3Nr)+EF_aLl8YTjF)Ij%?9L&f)+>Mz;sd7j zSKh&@_om6lNqHF}xvw@6z9aCu7w_q=<~uP_K=#gs;vIzudFenUhSP?ouyU9kaP)qi^aXsrV^Hi0uK!~57|y2;si+Ac~v-e$d44HUXo%V{Mp37v_i zJz!oWKt#QmyhKW-!0gYXz88BY?GuDPOwdA2{C?ouKX}x|CIOSLl;wUkAiFWgZ|^vpo}s9nG5k%$ll|QT~{ANS)mg z4)Yh0EOm0U<4t@lUZnm=QM)0>vkwB1SRFg+;IFjijGtpNxIbu0bTCe%S0l^vFb$eL zWnv#f24nKrb{blUp*xXjU+ZI_(aw01ev;e-sa2;d`HE0SHGZFH*4&X$T&2UNvTE|) z(xDed@9d3_JJo(jcJ@gnKh~yg{KX2+!gk8XILGAdcJAn~1r|(S9TM{)az_vJKv?4E zm_MBfPkYl}@=Fv~kx>+r_QJl5EKXM_!=qEw zZbRwf;2=7~n=q!*(IX}zN5>sB*Hyw&P&m|{msX!QsTC35AX(w(Yo(xqC~n_!?vqo7 z@jZ9Nw>Ki?`_E*u)hL}?;U*!|Au)d%diKbM$K?izRV2rg8}m;=u7(ntMx1P$$pnj| z%r%@Z#sTK3wS*_;IS)u9;-Y>Hst1`S&22Sy1UcUSMn5*l1#QLJ=Kny ziR-1?MUlt@iSQ!V**CMQfT(KFOSK>`5Hp^+oLtn{`HO&JN2hy7rtF zs0@MVY_pze+Fx85C8;H0c$MEX?HH?2P|H(0^n}*_%6vTKzTt2c8t29ZcO! z{=TI&F|u-Y05Z`tanN%DDJ@-H9bLE?82*)O;cVn+X=UO<@8E1fMFnIK`HNGo4u5T= z>}_03jQ%>rM9%`${clEA|DOF%dENhJVC7&h`WFL%l%m|sjLa;IT+A#?oJ{OYtTc?w z6pV~i{~#fQu&{$CQ0H%d8G%e3e?8$~WMpIkax&7hu>ZYd0_p)7B%B@G9RKC~zm3Je zJu|2P8C0E(>|GpBTyOoKVvV`!z8c{ZLad2}sF?0D> zEn=Ro5-P6$c=peL7%~3qA|mw9c$paeP5-*}Z|8r&HZwa5=l>Yk`T74Fh-bTL=_Qkw zBlwuf9a*1J@ zc=|y6f)Ok-rPAmkn?ZS%srY^M_KF_=TW+vVGh|x?41R@j}*YlGFvEe4&RE zu+x144oK_DC4<(8_Mmc8P&k|UrCo_Tuu8Yhw92+|&-aj9PT7^(vftdOuK=H6>3CI)K#z~dm=21=GpmCw`g~PgJ8}_*KA9yChEyh#>)Fh zAz#qEL{PiE=eHBVE4605=^z#LHS9Z|^}_6A8&ql#s2~Y({!eiaQMw}n6BD);=K`2r za3g=IHFN{vDDARA2DOTK@k0ygHS{(q3VZXAqSzr$N%8vT$bIoP5N?E=L;gR!L8HrK zXi7XEf;h(mes+pq`b^q4OUc?4&0MY&hw1nxdBK|fsw1e140d!M?FxZHy}|>m#jx^b z?Bq-Xl+X3Is{;fweb1jBcv}{5gWV(u;-1YW=C;Io?LUhmUbXjVMqTyAzW0m%iRPW< zMLV-#2|6?R==<%y2Z3nsL0BBtIfIJjFAKQLEsrUPkX1I`D1yXevhs*C(V1s;CK%ms z`=t>WhFuS4;NJH6^2;+o3G4j|F!E9y9S1%`$6|rJwhboCx;Y^}`y&E1&?LLM%tM6N z!VIP=*bKavtxGr5Kp9`)R(+EH3rZo7b0l7p=L1U&93@G2PoA_YNMbgBmhHIbY@#!K zz!@F80)Y*=Cjq`gpOwEgS?^Jh!=5vuyf~!{Sx0z-bGZt9|M{(lxG
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d'Évry}} + + \makeindex + \makeglossaries + +\usepackage{minted} \author{Samuel Ortion} \date{2023-2024} -\title{Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes\\\medskip -\large Scientific project} +\title{Further development on Finder, a pipeline to identify Tandem Arrayed Genes} \hypersetup{ pdfauthor={Samuel Ortion}, - pdftitle={Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes}, + pdftitle={Further development on Finder, a pipeline to identify Tandem Arrayed Genes}, pdfkeywords={}, pdfsubject={}, pdfcreator={Emacs 29.2 (Org mode 9.7)}, @@ -18,6 +25,87 @@ \begin{document} \maketitle +\hypersetup{ + pdfauthor={Samuel Ortion}, + pdftitle={}, + pdfkeywords={duplicate genes, workflow management systems, pipeline}, +} +\pagenumbering{roman} +\begin{abstract} +Duplicate genes is an important component of genomes. They have a particular role in genome evolution, allowing species to explore new gene functionality offering a pool of usable genes to build on. +TODO: +\end{abstract} + +\begin{center} +\textbf{keywords}: duplicate genes, tandem arrayed genes, pipeline +\end{center} + \tableofcontents +\printglossaries + +\pagenumbering{arabic} +\part{Context} +\label{sec:org8d0fa24} +\chapter{What are duplicate genes?} +\label{sec:orgee68751} +Duplicate genes are genes that experienced a duplication event during species evolution. + +These are homologous genes. +\section{Duplication mechanisms} +\label{sec:orgcf44cad} +\begin{center} +\includegraphics[width=.9\linewidth]{./figures/lallemand2020-fig1_copy.pdf} +\caption{\label{fig:gene-duplication-mechanisms}Mechanisms leading to gene duplication} +\end{center} +Several mechanisms may lead to gene duplication. We review them in this section. +\subsection{Segment duplication} +\label{sec:org922a1dd} +\subsection{Retroduplication} +\label{sec:orgd8f7e18} +Transposable elements cause an important part of gene duplication [citation needed] +Retrotransposon, or RNA transposon is one type of transposable element. Some of the representant of retrotransposon are similar to retroviruses. +Retrotransposon may be duplicated in the genome through a mechanism known as ``copy-and-paste''. +These transposons are typically composed of a reverse transcriptase gene. The protein encoded by this gene may proceed in the reverse transcription of the RNA transcript of the transposon sequence resulting in a DNA sequence which can then be included elsewhere in the genome. +During this process, the RNA transcript may include nearby gene sequence, which can thus be copied and pasted along with the retrotransposon. +\subsection{Transduplication} +\label{sec:org74a527a} +DNA transposon is an other type of transposable element whose transposition mechanisms can lead to gene duplication too. +This type of transposable element moves in the genome through a mechanisms known as ``cut-and-paste''. +The typical DNA transposon contains a transposase gene. The protein encoded by this gene recognize two sites surrounding the donnor transposon sequence in the chromosome resulting in a DNA cleavage. The transposase can then insert the transposon in a new place of the genome. +Similarly to retrotransposon, if a gene was present between the two cleavage sites of the donnor transposon, it may move with the transposed sequence. +\subsection{Tandem Duplication} +\label{sec:org1185c12} +\subsection{Polyploidisation} +\label{sec:org349eaa4} +\subsubsection{Alloployploïdisation} +\label{sec:org323512f} +\subsubsection{Autopolyploïdisation} +\label{sec:orgba5b73e} +\subsubsection{Mechanisms} +\label{sec:orga1009de} +\paragraph{Polyspermy} +\label{sec:orgee32a5c} +\paragraph{Non-reduced gametes} +\label{sec:org3297de6} +\subsection{Unequal crossing-over} +\label{sec:org31e5f76} +A crossing-over may occur during cell division. A fragment of chromosome is exchanged between two chromatids of a pair of chromosome. If the cleavage of the two chromatids occured at different positions on both chromosomes, the shared fragments may have different lengths. When the repair of missing fragment is performed, the resulting chromosome will incorporate a duplicate region of the chromosome, leading to a potential duplication for genes present in this region, as represented in figure \ref{fig:gene-duplication-mechanisms} B. \# TODO: check that this is really the B subfigure +\section{Role in genome evolution} +\label{sec:orga7bdfd9} +\chapter{Identification of duplicate genes} +\label{sec:org3aec87b} +\textbf{*} +\section{Finder} +\label{sec:org9b93040} +\part{Objectives} +\label{sec:org1b30340} +\chapter{Amend the existing Galaxy pipeline} +\label{sec:orgf108b0f} +Last year, a M1 student, Seanna Charles, worked on the Galaxy's version of the gls: Finder pipeline \autocite{charlesFinalisationPipelineFTAG2023}. +During my internship, I will continue this work. +\chapter{Porting Finder pipeline on a workflow manager} +\label{sec:orgd5c8063} + +\printbibliography \end{document} diff --git a/sty/lamme2024.sty b/sty/lamme2024.sty index 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\orcidlink{0009-0001-0971-497X} + \Large Samuel ORTION \orcidlink{0009-0001-0971-497X} \vfill \LARGE - - Development of a Nextflow\footnote{We still need to decide which workflow manager to choose: Nextflow or Snakemake} pipeline for FTAG Finder, a duplicate gene detection tool, and improvement of the existing Galaxy implementation + \makeatletter + \@title + \makeatother \vfill \normalsize