'Candidatus Phytoplasma phoenicium’ associated with almond witches’-broom disease: from draft genome to genetic diversity among strain populations

BACKGROUND: Almond witches'-broom (AlmWB), a devastating disease of almond, peach and nectarine in Lebanon, is associated with 'Candidatus Phytoplasma phoenicium'. In the present study, we generated a draft genome sequence of 'Ca. P. phoenicium' strain SA213, representative of phytoplasma strain populations from different host plants, and determined the genetic diversity among phytoplasma strain populations by phylogenetic analyses of 16S rRNA, groEL, tufB and inmp gene sequences. RESULTS: Sequence-based typing and phylogenetic analysis of the gene inmp, coding an integral membrane protein, distinguished AlmWB-associated phytoplasma strains originating from diverse host plants, whereas their 16S rRNA, tufB and groEL genes shared 100 % sequence identity. Moreover, dN/dS analysis indicated positive selection acting on inmp gene. Additionally, the analysis of 'Ca. P. phoenicium' draft genome revealed the presence of integral membrane proteins and effector-like proteins and potential candidates for interaction with hosts. One of the integral membrane proteins was predicted as BI-1, an inhibitor of apoptosis-promoting Bax factor. Bioinformatics analyses revealed the presence of putative BI-1 in draft and complete genomes of other 'Ca. Phytoplasma' species. CONCLUSION: The genetic diversity within 'Ca. P. phoenicium' strain populations in Lebanon suggested that AlmWB disease could be associated with phytoplasma strains derived from the adaptation of an original strain to diverse hosts. Moreover, the identification of a putative inhibitor of apoptosis-promoting Bax factor (BI-1) in 'Ca. P. phoenicium' draft genome and within genomes of other 'Ca. Phytoplasma' species suggested its potential role as a phytoplasma fitness-increasing factor by modification of the host-defense response

Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia

There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages

The fossil tragulids of the Siwalik Formations of Southern Asia

Tragulids are common in the Early Miocene through Pliocene Siwalik faunas of the Indian Subcontinent where they are represented by as many as 17 species. Large collections of Siwalik fossils have recently been made by collaborative projects from Harvard University, the University of Arizona, the Geological Survey of Pakistan, and the Pakistan Museum of Natural History. The collections together comprise over 3700 specimens, including dental, cranial, and postcranial elements. Most of this fossil material is from northern and southwestern Pakistan from well-dated stratigraphic sections. The oldest definite tragulids are from the Early Miocene Vihowa Formation and are around 18.7 Ma, while the youngest are in the Pliocene Tatrot Formation and are 3.3 Ma. The fossil tragulids of the Siwaliks differ from the extant species in a number of ways. Importantly, they have a much wider range of body sizes, ranging from 1 to nearly 76 kg. Consequently the small species overlap with the smallest species of extant Tragulus, while the large species approach medium size bovids and cervids. Compared to other ruminants, Siwalik tragulids are also relatively abundant and species rich. Although the status of some described species is uncertain, preliminary analysis indicates there are many as yet undescribed species. Three genera are known and typically at least four species co-exist at any one time during the Miocene. The history of the south Asian tragulids can be correlated to documented environmental changes. The Siwalik deposits formed in a large fluvial system, with mostly forested or wooded low relief floodplains having abundant cover and fruit. Isotopic analyses of tooth enamel and soil carbonates indicate the vegetation was dominated by C3 plants until 9 Ma, after which there was a shift to a more seasonally dry monsoon climate, undoubtedly accounting for a Late Miocene change in the relative abundance of tragulids