Some chloroplast assemblies can be tricky because of an inverted and duplicated region. I'm not sure if this applies to your system, but I've heard complaints about it from botanists wading into HTS. Different assemblers will produce different results, so you might need to try a few and mess around with the settings a bit. Have you tried mapping your contigs back to a reference of some sort? Perhaps differential coverage is breaking up your assembly into multiple pieces and things are more-or-less okay; perhaps other things are going on.
The Milkweed Genome Project has a pipeline that passes arguments to several programs and might help out. Alternatively, I'd try using a reference-guided assembly if you can use a not-too-distant reference.
I also recommend ARC for breaking down the complex genome assembly problem into a more manageable one focusing on just reads that share similarity with the chloroplast. I've had great success with this for mammalian mitochondrial genomes, and others have used it for plastids.
Did you taxon-annotate your contigs? Is this 70kbp contig from your chloroplast? I would say a 70kbp contig for a chloroplast is a good contig, given that IR will rarely be correctly assembled with NGS short reads. By the way, which insert size and read length did you use?
Did you try the suggestions from this thread?
Firstly, thanks for your answer... I did not annotate the contigs, is it necessary to get complete chloroplast or mitochondrial genome seq?
yes, the 70Kbp from the plant chloroplast that I sequenced after blast it to NCBI. but the complete chloroplast should come up to nearly 120-150 Kbp!!?
for this seq. I used Illumina Miseq 2x 150 mid-length.