<?xml version="1.0" encoding="ISO-8859-1"?><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<front>
<journal-meta>
<journal-id>2007-4298</journal-id>
<journal-title><![CDATA[Botanical Sciences]]></journal-title>
<abbrev-journal-title><![CDATA[Bot. sci]]></abbrev-journal-title>
<issn>2007-4298</issn>
<publisher>
<publisher-name><![CDATA[Sociedad Botánica de México A.C.]]></publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id>S2007-42982022000500083</article-id>
<article-id pub-id-type="doi">10.17129/botsci.3112</article-id>
<title-group>
<article-title xml:lang="en"><![CDATA[Perspectives in plant evolutionary genetics: A field guide in 15 &#8220;easy steps&#8221; to modern tools in evolutionary genetics and genomics]]></article-title>
<article-title xml:lang="es"><![CDATA[Perspectivas en genética evolutiva de plantas: Una guía de campo en 15 &#8220;sencillos pasos&#8221; a las herramientas modernas de la genética evolutiva y la genómica]]></article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Eguiarte]]></surname>
<given-names><![CDATA[Luis E.]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Aguirre-Planter]]></surname>
<given-names><![CDATA[Erika]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Castellanos-Morales]]></surname>
<given-names><![CDATA[Gabriela]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Souza]]></surname>
<given-names><![CDATA[Valeria]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
<xref ref-type="aff" rid="Aaf"/>
</contrib>
</contrib-group>
<aff id="Af1">
<institution><![CDATA[,Universidad Nacional Autónoma de México Instituto de Ecología Departamento de Ecología Evolutiva]]></institution>
<addr-line><![CDATA[ Ciudad de México]]></addr-line>
<country>Mexico</country>
</aff>
<aff id="Af2">
<institution><![CDATA[,El Colegio de la Frontera Sur Departamento de Conservación de la Biodiversidad ]]></institution>
<addr-line><![CDATA[Villahermosa Tabasco]]></addr-line>
<country>Mexico</country>
</aff>
<aff id="Af3">
<institution><![CDATA[,Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica  ]]></institution>
<addr-line><![CDATA[Punta Arenas ]]></addr-line>
<country>Chile</country>
</aff>
<pub-date pub-type="pub">
<day>00</day>
<month>00</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="epub">
<day>00</day>
<month>00</month>
<year>2022</year>
</pub-date>
<volume>100</volume>
<numero>spe</numero>
<fpage>83</fpage>
<lpage>109</lpage>
<copyright-statement/>
<copyright-year/>
<self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_arttext&amp;pid=S2007-42982022000500083&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_abstract&amp;pid=S2007-42982022000500083&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_pdf&amp;pid=S2007-42982022000500083&amp;lng=en&amp;nrm=iso"></self-uri><abstract abstract-type="short" xml:lang="en"><p><![CDATA[Abstract Plant genomes contain huge troves of information, and nowadays molecular tools to analyze genomes are less expensive and keep improving. In this review, we aimed to produce a &#8220;roadmap&#8221; to take advantage of this explosion of molecular methods and opportunities. We explain how to decide which strategies are adequate for a given evolutionary or taxonomic problem by describing 15 possible (and in some cases nonconsecutive) steps to take advantage of all the genomic resources drawing from the ever-increasing studies. We describe how to obtain an adequate genome sequence given our study species and objectives and discuss if we need to also obtain a transcriptome and additional &#8220;omic&#8221; data (i.e., proteome, metabolome, epigenome, microbiome). We analyze what is needed to conduct population genomics studies in terms of genomic methods and sampling strategies and discuss the pangenome concept. In addition, we present some considerations about how to estimate population genetics parameters and how to analyze geographic differentiation, inbreeding and gene flow. We examine ideas and methods on how to estimate natural selection and local adaptation, how to detect candidate genes, how coalescent analyses can help in these studies, the importance of genomic information for conservation studies and to understand adaptability to climate change. We assess the use of these methods in domestication studies and in understanding how form and function can be inferred from genes; likewise, how to use the genomic information for improvement of cultivated plants. We also review how can we use these methods in phylogenomic studies.]]></p></abstract>
<abstract abstract-type="short" xml:lang="es"><p><![CDATA[Resumen Los genomas vegetales contienen gran cantidad de información y las herramientas moleculares para analizarlos son cada vez más económicas y continúan mejorando. Presentamos un &#8220;mapa de ruta&#8221; para aprovechar esta explosión de métodos moleculares. Explicamos cómo decidir cuál es la estrategia adecuada para abordar un problema evolutivo o taxonómico a partir de 15 posibles (y en ocasiones no consecutivos) pasos para aprovechar los recursos genómicos disponibles. Describimos cómo obtener una secuencia genómica adecuada considerando la especie y los objetivos del estudio, y discutimos si se requiere obtener datos de transcriptoma u &#8220;ómicos&#8221; adicionales (p. ej., proteoma, metaboloma, epigenoma, microbioma). Analizamos qué se necesita para hacer estudios de genómica poblacional en términos de los posibles métodos genómicos y las estrategias de muestreo y discutimos el concepto del pangenoma. Además, presentamos algunas consideraciones sobre cómo estimar parámetros genéticos poblacionales y cómo analizar la diferenciación genética, la endogamia y el flujo génico. Examinamos ideas y métodos para estimar la selección natural y la adaptación local, para detectar genes candidatos, y reflexionamos sobre cómo los análisis coalescentes pueden ayudar en estos estudios, así como sobre la importancia de la información genómica en estudios de conservación y para comprender la adaptabilidad ante el cambio climático. Evaluamos cómo la forma y la función pueden inferirse a partir de los genes. Adicionalmente, discutimos como el uso de la información genómica puede servir para el mejoramiento de plantas cultivadas y en estudios de domesticación. También revisamos el uso de estos métodos en estudios filogenómicos.]]></p></abstract>
<kwd-group>
<kwd lng="en"><![CDATA[Adaptation]]></kwd>
<kwd lng="en"><![CDATA[Coalescence]]></kwd>
<kwd lng="en"><![CDATA[Conservation genomics]]></kwd>
<kwd lng="en"><![CDATA[Massive parallel sequencing]]></kwd>
<kwd lng="en"><![CDATA[Pangenome]]></kwd>
<kwd lng="en"><![CDATA[Population genomics]]></kwd>
<kwd lng="es"><![CDATA[Adaptación]]></kwd>
<kwd lng="es"><![CDATA[Coalescencia]]></kwd>
<kwd lng="es"><![CDATA[Genómica de poblaciones]]></kwd>
<kwd lng="es"><![CDATA[Genómica para la conservación]]></kwd>
<kwd lng="es"><![CDATA[Pangenoma]]></kwd>
<kwd lng="es"><![CDATA[Secuenciación paralela masiva]]></kwd>
</kwd-group>
</article-meta>
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<article-title xml:lang=""><![CDATA[Sequencing and assembly of the 22-Gb loblolly pine genome]]></article-title>
<source><![CDATA[Genetics]]></source>
<year>2014</year>
<volume>196</volume>
<page-range>875-90</page-range></nlm-citation>
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</article>
