James A. Langeland

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.

An amphioxus snail gene: Expression in paraxial mesoderm and neural plate suggests a conserved role in patterning the chordate embryo

Abstract Homologs of the Drosophilasnail gene have been characterized in several vertebrates. In addition to being expressed in mesoderm during gastrulation, vertebrate snail genes are also expressed in presumptive neural crest and/or its derivatives. Given that neural crest is unique to vertebrates and is considered to be of fundamental importance in their evolution, we have cloned and characterized the expression of a snail gene from amphioxus, a cephalochordate widely accepted as the sister group of the vertebrates. We show that, at the amino acid sequence level, the amphioxus snail gene is a clear phylogenetic outgroup to all the characterized vertebrate snail genes. During embryogenesis snail expression initially becomes restricted to the paraxial or presomitic mesoderm of amphioxus. Later, snail is expressed at high levels in the lateral neural plate, where it persists during neurulation. Our results indicate that an ancestral function of snail genes in the lineage leading to vertebrates is to define the paraxial mesoderm. Furthermore, our results indicate that a cell population homologous to the vertebrate neural crest may be present in amphioxus, thus providing an important link in the evolution of this key vertebrate tissue.

Amphioxus goosecoid and the evolution of the head organizer and prechordal plate

SUMMARY The organizer is a central feature of vertebrate embryogenesis and is functionally subdivided into the head organizer that gives rise primarily to the prechordal plate and induces forebrain structures, and the trunk/tail organizer that gives rise primarily to the notochord and induces more posterior structures. Goosecoid (gsc) encodes a homeodomain‐containing transcription factor that is expressed in the vertebrate head organizer and prechordal plate, and can induce a secondary axis when expressed ectopically. To investigate the evolution of the vertebrate head organizer and prechordal plate, we have cloned and characterized a gsc homolog from the cephalochordate amphioxus. Amphioxus, it is important to note, lacks a prechordal plate in that the notochord extends to the extreme anterior end of the animal, and lacks elaborate differentiation of its forebrain. Gsc expression in amphioxus is initially localized during gastrulation to the mesendodermal layer of the dorsal lip of the blastopore. However, gsc expression in amphioxus is not maintained in anterior axial mesoderm, as is the case with the vertebrate prechordal plate. Rather, gsc is expressed in the dorsal axial mesoderm of the blastopore lip throughout gastrulation, appearing transiently in the presumptive notochord that underlies all regions of the amphioxus brain. The similarities in gsc expression in amphioxus and vertebrates suggest that a primitive version of the head organizer evolved prior to the origin of the vertebrates. The differences in gsc expression can be interpreted either as the loss of the prechordal plate domain in the cephalochordate lineage, or the gain of a distinct gsc‐expressing prechordal plate that plays a role in forebrain induction in the vertebrate lineage.

Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource‐stretched setting has not been an option. Furthermore, we believe that a true interdisciplinary science experience would be best served by introduction of bioinformatics modules within existing courses in biology and chemistry and other complementary departments. To that end, with support from the Howard Hughes Medical Institute, we have developed over a dozen independent bioinformatics modules for our students that are incorporated into courses ranging from general chemistry and biology, advanced specialty courses, and classes in complementary disciplines such as computer science, mathematics, and physics. These activities have largely promoted active learning in our classrooms and have enhanced student understanding of course materials. Herein, we describe our program, the activities we have developed, and assessment of our endeavors in this area.

Patterns and consequences of vertebrate Emx gene duplications.

SUMMARY We have cloned and analyzed two Emx genes from the lamprey Petromyzon marinus and our findings provide insight into the patterns and developmental consequences of gene duplications during early vertebrate evolution. The Emx gene family presents an excellent case for addressing these issues as gnathostome vertebrates possess two or three Emx paralogs that are highly pleiotropic, functioning in or being expressed during the development of several vertebrate synapomorphies. Lampreys are the most primitive extant vertebrates and characterization of their development and genomic organization is critical for understanding vertebrate origins. We identified two Emx genes from P. marinus and analyzed their phylogeny and their embryological expression relative to other chordate Emx genes. Our phylogenetic analysis shows that the two lamprey Emx genes group independently from the gnathostome Emx1, Emx2, and Emx3 paralogy groups. Our expression analysis shows that the two lamprey Emx genes are expressed in distinct spatial and temporal patterns that together broadly encompass the combined sites of expression of all gnathostome Emx genes. Our data support a model wherein large‐scale regulatory evolution of a single Emx gene occurred after the protochordate/vertebrate divergence, but before the vertebrate radiation. Both the lamprey and gnathostome lineages then underwent independent gene duplications followed by extensive paralog subfunctionalization. Emx subfunctionalization in the telencephalon is remarkably convergent and refines our understanding of lamprey forebrain patterning. We also identify lamprey‐specific sites of expression that indicate either neofunctionalization in lampreys or sites‐specific nonfunctionalization of all gnathostome Emx genes. Overall, we see only very limited correlation between Emx gene duplications and the acquisition of novel expression domains.

Lamprey snail highlights conserved and novel patterning roles in vertebrate embryos

Abstractsnail genes mark presumptive mesoderm across bilaterian animals. In gnathostome vertebrates, snail genes are a multimember family that are also markers of premigratory neural crest (pnc) and some postmigratory neural crest derivatives in the pharyngeal arches. Previous studies of nonvertebrate chordates indicate that they have single snail genes that retain ancestral functions in mesoderm development and perhaps in specification of a pnc-like cell population. Lampreys are the most basal extant vertebrates, with well-defined developmental morphology. Here, we identify a single snail gene from the lamprey Petromyzon marinus that is the phylogenetic outgroup of all gnathostome snail genes. This single lamprey snail gene retains ancestral snail patterning domains present in nonvertebrate chordates. Lamprey snail is also expressed in tissues that are broadly equivalent to the combined sites of expression of all three gnathostome snail paralogy groups, excepting in embryonic tissues that are unique to gnathostomes. Importantly, while snail does not appear to demarcate an early neural crest population in lampreys as it does in gnathostomes, it may be involved in later neural crest development. Together, our results indicate that significant cis-regulatory innovation occurred in a single snail gene before the vertebrate radiation, and significant subfunctionalization occurred after snail gene duplications in the gnathostome lineages.

Asynchronous Evolutionary Origins of Aβ and BACE1

Neurodegenerative plaques characteristic of Alzheimers disease (AD) are composed of amyloid beta (Aβ) peptide, which is proteolyzed from amyloid precursor protein (APP) by β-secretase (beta-site APP cleaving enzyme [BACE1]) and γ-secretase. Although γ-secretase has essential functions across metazoans, no essential roles have been identified for BACE1 or Aβ. Because their only known function results in a disease phenotype, we sought to understand these components from an evolutionary perspective. We show that APP-like proteins are found throughout most animal taxa, but sequences homologous to Aβ are not found outside gnathostomes and the β cut site is only conserved within sarcopterygians. BACE1 enzymes, however, extend through basal chordates and as far as cnidaria. We then sought to determine whether BACE1 from a species that never evolved Aβ could proteolyze APP substrates that include Aβ. We demonstrate that BACE1 from a basal chordate is a functional ortholog that can liberate Aβ from full-length human APP, indicating BACE1 activity evolved at least 360 My before Aβ.

Evolution of retinoic acid receptors in chordates: insights from three lamprey species, Lampetra fluviatilis, Petromyzon marinus, and Lethenteron japonicum.

BackgroundRetinoic acid (RA) signaling controls many developmental processes in chordates, from early axis specification to late organogenesis. The functions of RA are chiefly mediated by a subfamily of nuclear hormone receptors, the retinoic acid receptors (RARs), that act as ligand-activated transcription factors. While RARs have been extensively studied in jawed vertebrates (that is, gnathostomes) and invertebrate chordates, very little is known about the repertoire and developmental roles of RARs in cyclostomes, which are extant jawless vertebrates. Here, we present the first extensive study of cyclostome RARs focusing on three different lamprey species: the European freshwater lamprey, Lampetra fluviatilis, the sea lamprey, Petromyzon marinus, and the Japanese lamprey, Lethenteron japonicum.ResultsWe identified four rar paralogs (rar1, rar2, rar3, and rar4) in each of the three lamprey species, and phylogenetic analyses indicate a complex evolutionary history of lamprey rar genes including the origin of rar1 and rar4 by lineage-specific duplication after the lamprey-hagfish split. We further assessed their expression patterns during embryonic development by in situ hybridization. The results show that lamprey rar genes are generally characterized by dynamic and highly specific expression domains in different embryonic tissues. In particular, lamprey rar genes exhibit combinatorial expression domains in the anterior central nervous system (CNS) and the pharyngeal region.ConclusionsOur results indicate that the genome of lampreys encodes at least four rar genes and suggest that the lamprey rar complement arose from vertebrate-specific whole genome duplications followed by a lamprey-specific duplication event. Moreover, we describe a combinatorial code of lamprey rar expression in both anterior CNS and pharynx resulting from dynamic and highly specific expression patterns during embryonic development. This ‘RAR code’ might function in regionalization and patterning of these two tissues by differentially modulating the expression of downstream effector genes during development.