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Genomics in the Journals May 22, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, a Chinese-led team presented findings from a genome sequencing study of the cultivated cotton plant Gossypium arboreum, which is believed to resemble the "A" sub-genome of tetraploid cotton species.

The researchers used a combination of whole-genome shotgun sequencing and bacterial artificial chromosome clone sequencing to tackle the diploid G. arboreum genome. After tacking the resulting sequences together into a 193.6 billion base assembly with almost 113-fold average coverage, they went on to annotate and investigate the genome.

The team's analysis defined 41,330 predicted protein-coding genes in the G. arboreum genome, along with hundreds of microRNAs, thousands of ribosomal-, transfer-, or small nuclear RNAs, and a slew of repetitive sequences.

By comparing the G. arboreum genome to sequences from other plants — including a G. raimondii plant sequenced by researchers at the Chinese Academy of Sciences and elsewhere in 2012 — the investigators gained insights into the biology and history of cotton plants. For example, the data pointed to at least two past whole-genome duplication events in the ancestor of both G. arboreum and G. raimondii.

Toxins found in centipede venom, while often distinct from those described in other venomous creatures, also includes a roster of similar venom proteins that evolved through convergent evolution, according to a Molecular Biology and Evolution study.

As part of their quest to understand venomous animal evolution, researchers from the University of Queensland and the Broad Institute did transcriptomic, phylogenetic, and proteomic analyses on five centipede species, which belong to an arthropod class called Chilopoda that emerged an estimated 440 million years ago.

By sequencing transcripts in the venom glands from the five centipede species, for example, the team tracked down dozens of different protein and peptide families in centipede venom, including many not known from studies of other venomous creatures.

Along with between-centipede venom comparisons, the study's authors looked at the apparent venom contributors in the context of other several stinging animals — from spiders and scorpions to the platypus and shrew — identifying differences and similarities in the ways toxin production systems have evolved in various animals.

"The presence of a wide range of novel proteins and peptides in centipede venoms highlights these animals as a rich source of novel bioactive molecules," the researchers wrote.

"Understanding the evolutionary processes behind these ancient venom systems will not only broaden our understanding of which traits make proteins and peptides amenable to neofunctionaliztaion," they added, "but it may also aid in directing bioprospecting efforts."

A genome sequencing study of the dampwood termite Zootermopsis nevadensis is providing new insights into the organism's biology and social organization.

As they reported in Nature Communications, members of a large, international team led by investigators in Germany, China, Denmark, and the US generated an almost 500 million base genome assembly for Z. nevadensis, along with transcriptomes from various dampwood termite caste and life cycle stages.

In an effort to understand the genetics behind the dampwood termite's social life — a caste system that includes reproductively active kings and sterile soldiers and workers — the team went on to compare the newly generated genomes and transcriptomes to sequences from Hymenoptera insects, an order that includes eusocial organisms such as ants and honey bees.

The analysis suggested the termite genome contains a bolstered set of genes involved in functions such as male fertility, but a diminished and divergent set of odor receptor genes, for example.

It also offered a look at the similarities and differences that exist in the genetics and epigenetics of sociality and caste determination in Z. nevadensis relative to those behind eusociality in ants and other Hymenoptera insects.

"These findings also show that you can't make assumptions about termites by studying ants — it's important to study both as comprehensively as possible," co-author Michael Roe, an entomology researcher at North Carolina State University, said in a statement.

Researchers from the US, Russia, and elsewhere sequenced and started analyzing the draft genome of a ctenophore called the Pacific sea gooseberry, Pleurobrachia bachei — work they described in Nature.

Together with transcriptome sequences from various P. bachei tissue types and developmental phases, the genome served as a source of information on animal evolution for the study's authors.

Their analyses supported the notion that the ctenophores such as the Pacific sea gooseberry and the comb jelly Mnemiopsis leidyi — which had its genome sequenced and described in Science last year — belong to the earliest branching metazoan animal lineage.

In particular, the team saw distinct sets of genes contributing to ctenophore development, immunity, and neural functions relative to those present in creatures from other branches of the animal tree, hinting at the possibility of parallel, independent evolution of nervous systems and other notable animal features.