This book is the first comprehensive compilation of the most up-to-date research in the genomics, transcriptomics, and breeding of pine species across Europe, North America, and Australia. With chapters on the state of the reference genomes, transposon function, genome-wide diversity, functional genomics, genomics of disease resistance, genomics of abiotic stress, and genomic selection, this book is a must-read for scientists, breeders, and students of plant genomics. The book contains 12 chapters over 300 pages authored by a group of world-renowned scientists in the field of pine genomics. Pines (Pinus) are the world’s most economically important forest tree species. The recent genome sequencing of several important pine species has paved the way for understanding their complex biology and helps future management and breeding efforts.

This book is the first comprehensive volume on conifers detailing their genomes, variations, and evolution. The book begins with general information about conifers such as taxonomy, geography, reproduction, life history, and social and economic importance. Then topics discussed include the full genome sequence, complex traits, phenotypic and genetic variations, landscape genomics, and forest health and conservation. This book also synthesizes the research included to provide a bigger picture and suggest an evolutionary trajectory. As a large plant family, conifers are an important part of economic botany. The group includes the pines, spruces, firs, larches, yews, junipers, cedars, cypresses, and sequoias. Of the phylum Coniferophyta, conifers typically bear cones and evergreen leaves. Recently, there has been much data available in conifer genomics with the publication of several crop and non-crop genome sequences. In addition to their economic importance, conifers are an important habitat for humans and animals, especially in developing parts of the world. The application of genomics for improving the productivity of conifer crops holds great promise to help provide resources for the most needy in the world.

HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.

This work is a comprehensive collection of articles that cover aspects of cell wall research in the genomic era. Some 2500 genes are involved in some way in wall biogenesis and turnover, from generation of substrates, to polysaccharide and lignin synthesis, assembly, and rearrangement in the wall. Although a great number of genes and gene families remain to be characterized, this issue provides a census of the genes that have been discovered so far. The articles comprising this issue not only illustrate the enormous progress made in identifying the wealth of wall-related genes but they also show the future directions and how far we have to go. As cell walls are an enormously important source of raw material, we anticipate that cell-wall-related genes are of significant economic importance. Examples include the modification of pectin-cross-linking or cell-cell adhesion to increase shelf life of fruits and vegetables, the enhancement of dietary fiber contents of cereals, the improvement of yield and quality of fibers, and the relative allocation of carbon to wall biomass for use as biofuels. The book is intended for academic and professional scientists working in the area of plant biology as well as material chemists and engineers, and food scientists who define new ways to use cell walls.

Forest tree improvement has mainly been implemented to enhance the productivity of artificial forests. However, given the drastically changing global environment, improvement of various traits related to environmental adaptability is more essential than ever. This book focuses on genetic information, including trait heritability and the physiological mechanisms thereof, which facilitate tree improvement. Nineteen papers are included, reporting genetic approaches to improving various species, including conifers, broad-leaf trees, and bamboo. All of the papers in this book provide cutting-edge genetic information on tree genetics and suggest research directions for future tree improvement.

In this timely new 2-volume treatise, experts from around the world have banded together to produce a first-of-its-kind synopsis of the exciting and fast moving field of plant evolutionary genomics. In Volume I of Plant Genome Diversity, an update is provided on what we have learned from plant genome sequencing projects. This is followed by more focused chapters on the various genomic “residents” of plant genomes, including transposable elements, centromeres, small RNAs, and the evolutionary dynamics of genes and non-coding sequences. Attention is drawn to advances in our understanding of plant mitochondrial and plastid genomes, as well as the significance of duplication in genic evolution and the non-independent evolution among sequences in plant genomes. Finally, Volume I provides an introduction to the vibrant new frontier of plant epigenomics, describing the current state of our knowledge and the evolutionary implications of the epigenomic landscape.