Chromosome Level Genome Assembly Reveals Cassia Tora May Be an Ancient Species in Leguminosae

Background: Cassia tora L. is an annual leguminous plant. Its seeds had wide utility in herbal medicine in Asian, but is usually regard as a potent, invasive weed which even helps farmers eliminate other parasitic weed species. However, compared with other important legume crops, C. tora is far from fully developed and the genetic basis is greatly lacking. A reference genome sequence will be great valuable resource for its genome evolution, genetic breeding and development.Results: Here, we de novo assembled a chromosome-scale genome for C. tora by combining PacBio sequencing technology with chromatin interaction mapping, resulting in 621-Mb genome with a contig N50 of 2.5 Mb, of which 77.44% was ordered and oriented on 13 pseudochromosomes. The genome contained 32,361 protein-coding genes with a repetitive DNA content of approximately 58.15%. Gypsy-type LTRs constituted the largest subfamily. LTR insertion events seldom occurred in this genome over the past 10 million years. Comparative genomic analyses showed that C. tora diverged ~95 million years ago (MYA), which revealed it has the most distant genetic relationship with 11 other legumes. Compared with other legume crops, Cassia tora is maybe an ancient species in Leguminosae.Conclusions: The high-quality reference genome sequence reported here furnishes unprecedented insights into genome dynamics and provides an important basis for future research on legume genome evolution.

A Reference Genome Sequence for Giant Sequoia

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, were used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers

The utility of the domestic cat as a model system for biomedical studies was constrained for many years by the absence of a comprehensive feline reference genome sequence assembly. While such a resource now exists, the cat continues to lag behind the domestic dog in terms of integration into the ‘One Health’ era of molecular medicine. Stimulated by the advances being made within the evolving field of comparative cancer genomics, we developed a microarray platform that allows rapid and sensitive detection of DNA copy number aberrations in feline tumors using comparative genomic hybridization analysis. The microarray comprises 110,456 unique oligonucleotide probes anchored at mean intervals of 22.6 kb throughout the feline reference genome sequence assembly, providing ~350-fold higher resolution than was previously possible using this technique. We demonstrate the utility of this resource through genomic profiling of a feline injection-site sarcoma case, revealing a highly disrupted profile of DNA copy number imbalance involving several key cancer-associated genes including KIT, TP53, PTEN, FAS and RB1. These findings were supported by targeted fluorescence in-situ hybridization analysis, which identified major alterations in chromosome structure, including complex intrachromosomal reorganization events typical of those seen in aggressive soft-tissue sarcomas of other species. We then characterized a second mass that was identified at a nearby site in the same patient almost 12 months later. This mass demonstrated a remarkably conserved genomic profile consistent with a recurrence of the original tumor; however the detection of subtle differences reflected evolution of the tumor over time. These findings exemplify the diverse potential of this microarray platform to incorporate domestic cat cancers into comparative and translational research efforts in molecular oncology.

Genome sequence and analysis of the eggplant (Solanum melongena L.)

SummaryThe eggplant (Solanum melongena L.) is one of the most important Solanaceae crops, ranking third in the total production and economic value in the genus Solanum. Here, we report a high-quality, chromosome-scale eggplant reference genome sequence of 1,155.8 Mb, with N50 of 93.9 Mb, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences occupied 70.1% of the assembly length, and 35,018 high-confidence protein-coding genes were annotated based on multiple evidence. Comparative analysis revealed 646 species-specific families and 364 positive selection genes, conferring distinguishing traits to the eggplant. We performed genome-wide identification of disease resistance genes and discovered an expanded gene family of bacterial spot resistance in the eggplant and pepper but not in tomato and potato. The genes involved in chlorogenic acid synthesis were comprehensively characterized. Highly similar chromosomal distribution patterns of polyphenol oxidase genes were observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only facilitate evolutionary studies in the Solanaceae but also facilitate their breeding and improvement.

Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State

Coccidioides fungi are widely distributed in the American continents, with an expanding western range documented by a recently discovered cryptic population of Coccidioides immitis in Washington State. The assembled and annotated reference genome sequence of the soil-derived C. immitis strain WA_211 will support population and functional genomics studies.