Authors :

Arnaud Bellec, Audrey Courtial, Stephane Cauet, Nathalie Rodde, Sonia Vautrin, Genseric Beydon, Nadege Arnal, Nadine Gautier, Joelle Fourment, Elisa Prat, William Marande, Yves Barriere and Helene Berges.

Journal of Next Generation Sequencing & Applications.

Abstract :

Background:
Numerous completed or on-going whole genome sequencing projects have highlighted the fact that obtaining a high quality genome sequence is necessary to address comparative genomics questions such as structural variations among genotypes and gain or loss of specific function. Despite the spectacular progress that has been made in sequencing technologies, obtaining accurate and reliable data is still a challenge, both at the whole genome scale and when targeting specific genomic regions. These problems are even more noticeable for complex plant genomes. Most plant genomes are known to be particularly challenging due to their size, high density of repetitive elements and various levels of ploidy. To overcome these problems, we have developed a strategy to reduce genome complexity by using the large insert BAC libraries combined with next generation sequencing technologies.

Results:
We compared two different technologies (Roche-454 and Pacific Biosciences PacBio RS II) to sequence pools of BAC clones in order to obtain the best quality sequence. We targeted nine BAC clones from different species (maize, wheat, strawberry, barley, sugarcane and sunflower) known to be complex in terms of sequence assembly. We sequenced the pools of the nine BAC clones with both technologies. We compared assembly results and highlighted differences due to the sequencing technologies used.

Conclusions:
We demonstrated that the long reads obtained with the PacBio RS II technology serve to obtain a better and more reliable assembly, notably by preventing errors due to duplicated or repetitive sequences in the same region.

Link :

http://www.omicsonline.org/open-access/long-read-sequencing-technology-to-solve-complex-genomic-regionsassembly-in-plants-2469-9853-1000128.pdf

Authors

Lloyd A, Ranoux M, Vautrin S, Glover N, Fourment J, Charif D, Choulet F, Lassalle G, Marande W, Tran J, Granier F, Pingault L, Remay A, Marquis C, Belcram H, Chalhoub B, Feuillet C, Bergès H, Sourdille P, Jenczewski E.

MolBiol Evol. 2014

Abstract

Meiosis, the basis of sex, evolved through iterative gene duplications. To understand whether subsequent duplications have further enriched the core meiotic "tool-kit", we investigated the fate of meiotic gene duplicates following Whole Genome Duplication (WGD), a common occurrence in eukaryotes. We show that meiotic genes return to a single copy more rapidly than genome-wide average in Angiosperms, one of the lineages in which WGD is most vividly exemplified. The rate at which duplicates are lost decreases through time, a tendency that is also observed genome-wide and may thus prove to be a general trend post-WGD. The sharpest decline is observed for the subset of genes mediating meiotic recombination; however, we found no evidence that the presence of these duplicates is counter-selected in two recent polyploid crops selected for fertility. We therefore propose that their loss is passive, highlighting how quickly WGDs are resolved in the absence of selective duplicate retention.

http://www.ncbi.nlm.nih.gov/pubmed/24694832

Authors

Ferreira de Carvalho J, Chelaifa H, Boutte J, Poulain J, Couloux A, Wincker P, Bellec A, Fourment J, Bergès H, Salmon A, Ainouche M.

Plant Mol Biol. 2013 Jul 23

Abstract

Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91 % of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67 %). Non-LTR retrotransposons represent 0.75 %, DNA transposons 0.99 %, whereas small RNA, simple repeats and low-complexity sequences account for 1.38 % of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1 % of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6 % of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family.

Link

http://www.ncbi.nlm.nih.gov/pubmed/23877482